Warning. This John who married Anne Merrill, both of whom were buried in Edworth, wasn't the son of John and Christian of South Mylls, who did have a son, John who married Anne Clarke. Neither is he anything to do with John Spencer of Althorp in Northampton.
John Spencer, whose parents and birthplace have not been identified, was born probably within a few years after 1500 in Bedfordshire, probably in the village of Edworth.
They had the following three sons:
John died and was buried at Edworth, on 9 June 1558, as John Spencer senior.; 
Feb 12, 2018 Update by Robert Spencer UEL, hope this clarifies things on the issue of the wife of John Spencer of Edworth, as new information eliminates Anne Clarke as a wife, she is named in a will of another John Spencer, who resided in London, with many children and was well documented in church records there. I'm not sure she's mentioned by name in any document!
The will of John Spencer's widow, dated 13 June 1560, proved 21 Apr 1561, includes the following: brother Edward's children, to have the £1 that he borrowed of her, and the barley he gave her sons to his children; Nicholas Merryll and John Merryll his brother, to have the barley their father gave her sons... "From the terms of the will, it would seem that Anne's brother was Edward Merryll or Merrill, and that this was her maiden name. A search of Merrill wills might confirm this conjecture."
The will of John Merell, husbandman of Biggleswade, made 12 Oct 1558, proved 5 Dec 1558, mentions his brother Edward Morell of Stratton; his sons Nicholas and John (compare with Ann Spencer's 1560 will), and just to confirm the hypothesis "To his brother Spenser's children at Edworth a quarter of barley each." which ties in with Anne's will "Nicholas Merryll and John Merryll his brother, to have the barley their father gave her sons..."
The other thing that strikes me about the Edworth family are the names - they don't fit the naming pattern of the Blunham/Eaton Socon Spencers who only named their sons John or Robert! eg Michael and Gerard Could this indicate they were of different Spencer stock?
John Spencer left no will that has been traced, but his widow did:
from Anne's will dated 13 Jun 1560, proved 21 Apr 1561, she mentioned her son Gerard (aged 17); son Michael to have the chest that was his brother John's; John Spencer, son Michael's child, to have £20. Jacobus  gained the impression that "our Spencer family at that period was of the yeoman class, and somewhat better off than the average village family of the time and place. Whether they were in origin a younger branch of an older gentry family, or a more humble clan which by industry and good fortune had improved its lot, we are not in a position to affirm. It would be necessary to prove the parentage and more remote ancestry of John Spencer, Sr., by documentary evidence, before claiming any specific connection with any other Spencer family in England." So Jacobus is saying that the parents of John who died in 1558 aren't known.
According to the Rev. Holding, John was a son of John Spencer of South Mylls.Source? From an extensive search of records in Bedfordshire Mr Holding ascertained to his satisfaction that John Spencer, the 18th in descent from Robert the steward of King William, was the John Spencer who resided at St.Albans, England in 1553, and who later moved to Kempston and Edworth, Bedfordshire, and is the ancestor of the Massachusetts and Connecticut Spencers. In the year 1553 a Royal charter was given to the town of St. Albans by Edward VI. One of the chief burgesses or alderman was John Spencer. Shortly afterwards he moved to Edworth, (evidence?)where he died a few years later, in 1558, and where his family resided. The previous sentence says he moved first to Kempston before moving to Edworth. Yet John Spencer of Kempston is mentioned in John Spencer of Pavenham's 1531 will, so he was in Kempston much earlier than is supposed in this biography
The John Spencer in St Albans is much more likely to be John, of South Mills and Bramfield, who possibly travelled to St Albans stopping off in Kempston on the way. It would explain the link to John of Pavenham who died in 1532 John
From research made by Mr. Holding it appears that John Spencer occupied a farm of about 600 acres at Edworth, as lessee of Robert Parry of Ellington, who was then lord of the Manor. Are there any dates which might help fix when he allegedly moved from St Albans? Writing of the will of Anne Spencer, Mr Holding says: "It is interesting as showing the position in life she occupied, and her kindly, thought nature. The enumeration of stock and chattels, and her bequests certainly show that the family was at least that of a prosperous gentleman." "She nowhere makes mention of land or tenements belonging to her. There is only the lease of the farm which evidently refers to the ones of which she was then the tenant, and which is handed on to her oldest son Michael." Regarding the Edworth farm Mr Holding says: "Edworth is a parish on the borders of Hertfordshire, and is situated half way between Baldock and Biggleswade. There have always been two large farms in Edworth, comprising really the whole land in the parish, with the exception of about 8 acres glebeland attached to the rectory, giving a total of about 1122 acres." "So that the Spencer farm would cover about 600 acres in extent, a large farm even at that present time, and gave employment to half the laboring poor of the place. The Hall, where the Spencers resided, is still standing, although much modernized. what's the evidence they lived at the Hall? The evidence is that others lived at the manor house There is none: these Spencers are yeoman farmers and husbandmen, not gentlefolk. While clearly comfortably off, the wills make it clear they are prosperous farmers.
In 1923, H.R. Spencer, author of the Spencers of East Haddam, visited Edworth. The old church is still standing, in the same shape as when John and Anne Spencer worshiped there. The old baptismal font is still in use - the same font at which the Spencer children were christened. The church register is still in a good state of preservation, and dates back several hundred years prior to the time when John and Anne Spencer resided there. Utter piffle! The parish register only starts in 1552, probably AFTER John and Anne began residing there. Original entries show the dates of christening of Michael Spencer's children, and the date of the burials of both John and Anne Spencer. There is nothing in the churchyard to indicate at what precise spot John and his wife are buried. On the interior wall of the church H.R. Spencer placed a brass tablet containing the words: In Memoriam John and Anne Spencer 1558-1560.
In the absence of baptisms, it is quite probable that Michael Spencer of Edworth and Gerrard Spencer of Biggleswade were sons of John Spencer Senior and Ann Spencer whose burials are recorded in Edworth register the former June 9 1558 and the latter June 16 1560, given the evidence provided by Anne's will. Nothing more is known of them other than what is disclosed by these records and the absence of further information may be accounted for by the fact that Edworth registers do not extend back beyond 1552 and that many wills and valuable records and documents it is said (by whom?) were destroyed during the civil war. IF it was John Spencer of St Albans who moved to Edworth after 1553 the three sons would all have been born in St Albans. But I have seen no evidence that it was the same John.
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