Charles Edward Louis John Casimir Sylvester Severino Maria Stuart (31 December 1720 – 31 January 1788), commonly known in Britain during his lifetime as The Young Pretender and often known in retrospective accounts as Bonnie Prince Charlie, was the second Jacobite pretender to the thrones of England, Scotland, France and Ireland. Charles was the eldest son of James Francis Edward Stuart. Charles was born in the Palazzo Muti, Rome, Italy, on 31 December 1720, where his father had been given a residence by Pope Clement XI. He spent almost all his childhood in Rome and Bologna. 
Bonnie Prince Charlie, The Young Pretender, King of Great Britain (for only 6 weeks , at Hollyrood House))
The Jacobite Rising
Charles Edward Stuart's Jacobite invasion began with his landing in Scotland July. 1745 and ended with his defeat at the Battle of Culloden on 16 April 1746. and final departure of Scotland in September, 1746 when he sailed for France to safety and exile.  With the Jacobite cause now lost, Stuart would spend the remainder of his life — with one brief secret visit to London — in exile. 
Life as an Exile
While back in France, Charles had numerous affairs; the one with his first cousin Marie Louise de La Tour d'Auvergne, wife of Jules, Prince of Guéméné, resulted in a short-lived son Charles (1748–1749). In 1748 Charles was expelled from France under the terms of the Treaty of Aix-la-Chapelle which brought the war between Britain and France to an end 
Meeting and relationship with Clementina Walkinshaw
In 1746, Clementina was living at the home of her uncle Sir Hugh Paterson at Bannockburn, near Stirling. The Prince came to Sir Hugh's home in early January 1746 where he first met Clementina, and he returned later that month to be nursed by her from what appears to have been a cold. Given that she was living under her uncle's protection, it is not thought the two were lovers at this time. 
After the defeat of the Prince's rebellion at Culloden in April 1746, Charles fled Scotland for France. In the following years, he had a scandalous affair with his 22-year-old first cousin Louise de Montbazon (who was married to his close friend, and whom he deserted when she became pregnant) and then with the Princess of Talmont, who was in her 40s. In 1752, he heard that Clementina was at Dunkirk and in some financial difficulties, so he sent 50 louis d'or to help her and then dispatched Sir Henry Goring to entreat her to come to Ghent and live with him as his mistress. Goring, who described Clementina as a "bad woman", complained of being used as "no better than a pimp", and shortly after left Charles' employ. However, by November 1752, Clementina was living with Charles, and was to remain as his mistress for the following eight years. The couple moved to Liège where Charlotte, their only child, was born on 29 October 1753  and baptised into the Roman Catholic faith at the church of Sainte Marie-des-Fonts. 
From "Jacobite Rebellion of 1745" comes a slightly different view of their meeting. On 19 January 1746 Bonnie Prince Charlie went to the house of Sir Hugh Paterson at Bannockburn where Clementina was also staying. The Prince developed a feverish cold and during the illness was nursed back to health by Clementina. According to David Wemyss, Lord Elcho it was during this period that she became the mistress of Bonnie Prince Charlie. It would appear that he was slightly distracted at this point for in a letter on 23 January to Lord George Murray, he wrote: "I was just ready to get on horseback in order to make you a visit but have been over-persuaded to let it alone by people who are continuously teasing me with my cold." 
Apart from their acknowledged daughter, Charlotte, Clementina and Prince Charles had a son who died in infancy. There was speculation that another daughter was born to the couple but there is no corroboration to substantiate the birth. Little is known of Clementina Walkinshaw between 1746 & 1752. 
In 1752 Charles persuaded Clementina to come to France to live with him, Their relationship produced a daughter they named Charlotte. They lived together for eight years until increasing verbal and physical abuse forced her to run away taking their young daughter Charlotte with her. Although Charlotte was later reconciled with her father and lived with him for the last years of his life, her parents never met again. Clementine Walkinshaw outlived both Charles and her daughter, dying in genteel poverty in Switzerland in 1802. 
A previously Unknown Son ?
Although the history books say that Charlotte was the only child of Charles and Clementina that lived to maturity there is a family in New Zealand that claims that their ancestor, John Stuart was not only a son of Charles Stuart and Clementina, but that he married a descendant of the Douglases of Glenbervie and that he and his wife had a daughter. They point to old letters and family tradition passed on to them by their elderly grandparents as evidence of their claim. They also say they are in possession of a painting of Charles Edward Stuart that also contains an image of an infant thought to be John Stuart. But, is it even possible that Charles and Clementina had a son that lived to maturity and fathered a grandaughter of "The young Pretender". Historical evidence says no. But could it be possible in spite of the evidence ? Let's examine the claim in the light of known historical fact.
It is said by his living descendants that John Stuart was born in Scotland about 1747. At that time Charles Stuart would have been in France living there in exile after his embarrassing defeat in Scotland. Could it be possible that a year after his escape to France that he would have a son born in Scotland and he wouldn't be aware of it ? In 1746, Clementina. said to be John's mother, was living at the home of her uncle Sir Hugh Paterson at Bannockburn, near Stirling.  It is known that Charles, who was in Scotland trying to press his claim to the throne, came to visit Sir Hugh, a staunch Jacobite, early in January of 1746. There he met Clementina, Sir Hugh's niece for the first time. Charles became ill with a cold and returning to Sir Hugh's home later in January, was nursed back to health by the young Clementina. Some historians feel that they were not intimate at the time since Clementina was living in her uncles home and under his protection. However, in the "Jacobite Rebellion of 1745" a different view is brought forward. According to the author of this book, " On 19 January 1746 Bonnie Prince Charlie went to the house of Sir Hugh Paterson at Bannockburn where Clementina was also staying. The Prince developed a feverish cold and during the illness was nursed back to health by Clementina. According to David Wymss, Lord Elcho it was during this period that she became the mistress of Bonnie Prince Charlie." , So, there was the belief at that time in history by a contemporary of Charles that he and Clementina had been intimate early in 1746. 
History goes on to record that Charles lost his claim to the throne at his disasterous defeat at at the Battle of Culloden on 16 April 1746. A marked man with a price on his head, he was on the run and fearful of capture until his escape and final departure from Scotland in September, 1746 when he sailed for France. He never returned to England, except for a secret visit to London, years later.
It is assumed that Clementina remained in Scotland, but little is actually known of her life during this period. Is it possible that she gave birth to a son during that time ? If so, history fails to record the event. But, it is possible that Charles and Clementina had been intimate and she became pregnant and gave birth to a son in Scotland. Her family may have wanted to protect her and the child and so never made it known ? That is what John Stewart's descendants believe. It was also that during this time that Charles had a number of mistresses in France, resulting in the birth of a son, Charles. But sadly, the young son and heir of Charles Stuart was to die after living about a year.
The next time Charles hears of Clementina she is living at Dunkirk and in some financial difficulties, so he sent 50 louis d'or to help her and then dispatched Sir Henry Goring to entreat her to come to Ghent and live with him as his mistress. Goring advised him against it but by November 1752, Clementina was living with Charles, and was to remain as his mistress for the following eight years. The couple moved to Liège where Charlotte, which history says is their only child, was born on 29 October 1753  and baptised into the Roman Catholic faith at the church of Sainte Marie-des-Fonts. 
Did Clementina take John Stuart to France with her ? There is no mention of John Stuart living with Charles and Clementina. So, where is the elusive John Stuart, who would have been the only male heir of Charles Edward Stuart ? Could it be possible that Clementina left him in Scotland in care of her family, It is possible, although unproved. Perhaps, Clementina did not want to complicate things by bringing their illegitimate son into their renewed relationship. When Clementina gave birth to Charlotte, Charles refused for many years to recognize her as his child. It was only in his latter years, when he thought he was dying that he recognized Charlotte as his daughter and heir. In return she went to her father's side and stayed with him until his death. She left her three children with her mother, Clementina. Clementina was to outlive both Charles and Charlotte.
So the question is if Charles recognized Charlotte as his child, which history records, why would he not recognize a son, a child of the same mother, Clementina ? When Clementina went to live with Charles in France there is no indication of a son being with her. If she had a young son she probably left him in the care of her family in Scotland. John would have been 5 - 6 at that time. Before dismissing this one should remember that is exactly what Charlotte did when she went to care for her father in the last years of his life, Charlotte gave her three children into her mother's care and never saw them again. Perhaps we have the same situation with John ? Charles never learned of his grandchildren so it shouldn't be altogether surprising to know that he never knew of his illegitimate son, John Stuart. Perhaps some time passed before John Stuart learned the truth of who is father was. He wasn't raised by his mother and his father never knew he existed. It wouldn't have been until he was older that he would have learned the truth.
From "The Golden Falcon, Chap 4" we find that Charles returned to Rome on Jan 1,1766. Colonel Edmund Ryan, an Irish colonel in the French service was sent as Charles's agent in the marriage negotiations for the hand of Princess Louise of Stolberg-Gedern, descended from the families of Bruce of Scotland, Montgomery and Crequis of France, Orsini and Gonzagas of Italy and Medinas of Spain.
They married on April 17, 1772 at Macerata, but had no children although there was a persistent rumour that they had a son in 1775 in Leghorn (Livorno) or Siena. Napoleon asked Henry, Cardinal York about this child but he denied it. However the attempts at assassination by the English could have driven the last Stuarts to conceal the birth of a child. Clementina was in a convent for 2 years and so was Louise. 
So, this too is another reason that John's existence may have been concealed. Fear of reprisal by the English on the son of "The Young Pretender" Certainly this would have been a good reason to keep his existence and his whereabouts secret. It would be years before the existence of Charles daughter, Charlotte and her children were to become known to historians.
The descendants of John Stuart believe he is the son of Charles Edward Stuart. They do not have hard evidence of this relationship and historians would disagree with their claim. What they do have is a long family tradition passed down through the years and a strong personal belief that John Stuart is of Royal descent. They are hopeful that forthcoming DNA evidence will support their belief that Charles Stuart was the father of their ancestor, John Stuart. And in the meantime the search for documentary proofs will go on. If they do prove their claim, they know they will re-write history.
It has been determined in a scientific study in the UK that half of all the men who carry the surname of Stewart or Stuart are directly descended from royalty. 
DNA results normally can not be linked to a particular person but can show a probable relationship between two individuals when matching genetic markers are present. That means that those two individuals had a common ancestor at some point in history. Recently, a DNA testing program by Britains DNA – a genetic ancestry provider – has managed to identify the development of a genetic marker in a historical figure for the first time. This has led to the discovery that half of all men with the surname Stewart or Stuart are directly descended from Alexander the fourth, High Steward of Scotland. 
↑ Douglas, Hugh (2004) "Walkinshaw, Clementine, styled countess of Albestroff (c.1720–1802)", Oxford Dictionary of National Biography, Oxford University Press, doi:10.1093/ref:odnb/28523, retrieved 2007-12-14 (subscription required). The first edition of this text is available as an article on Wikisource: "Walkinshaw, Clementina". Dictionary of National Biography. London: Smith, Elder & Co. 1885–1900.
↑ Bonnie Prince Charlie by Fitzroy Maclean, page 168, published by Buttler and Tanner Ltd., London
↑ Damn' Rebel Bitches, The Women of the '45, by Maggie Craig, Mainstream Publishing, Edinburgh and London, 1997, page 71
↑britainsdna.com ROYAL SCOTLAND, ROYAL STEWART Britian's DNA project found that regardless of their family trees, 50% of all men who have the surname of Stewart or Stuart are the direct descendants of Scotland’s longlasting royal dynasty (who also came to rule over Britain and Ireland). This data has been derived from sampling of the general population by ScotlandsDNA, BritainsDNA, IrelandsDNA and YorkshiresDNA.
This page has been edited according to Style Standards adopted January 2014. Descriptions of imported gedcoms for this profile are under the Changes tab.
Clementina followed Charles to Europe, the child John Stewart / Stuart could easily have been born there , because there are no birth records ; only marriage & death , and probate. however , mysteriously John Stewart/ Stuart was married to Margaret Douglas Tower secretly in the mother's (Margaret Douglas) house by the HEAD BISHOP of the Episticol church of Scotland, I see this as odd and hidden from public maybe ?
their Daughter Margaret Douglas Stewart (born same year her father John died 1794) he was 47 at death , therefore born 1746/47, which fits perfectly with the time Clementina "Become undone" / her words; and when she was nursing Charles / became his mistress; or after following him to Europe some months after he escaped. he was known for using Psuedonums like Pitt & Chevalier , Johnson ( he used as parents on Charlotte's & possibly other children's birth certificate)
our family have since (2016) found one of the 3 (according to a letter) minatures; this one of Charles himself in his late 30's -40's it seams , a jewellery / pendant minature
the other possibility is Comtesse De Vasse as the was talk of this surname within family (I do have Vasse on matches surname list) (Jackie Stoddard)
It may be possible to confirm family relationships with Charles by comparing test results with other carriers of his Y-chromosome or his mother's mitochondrial DNA.
Y-chromosome DNA test-takers in his direct paternal line on WikiTree: