NOTE! Please do not add or link parents or siblings for John Funkhouser Sr. unless you have done research in old Swiss or colonial American records and found documents proving parentage and relationships to other Funkhousers or Fankhausers, and can cite those specific documents.
John Funkhouser is the English name for Johannes (Hans) Fankhauser, one of the three Fankhauser men who are considered founders of the Funkhouser families of America.  In spite of many efforts and endless hours of research by a number of historians and genealogists, and several erroneous assumptions, the relationship between Johannes, Jacob and Christian Fankhauser, the three pioneer founders, remains unknown and links to specific Swiss parents and ancestors are as elusive as ever.
A Funkhouser Y-DNA project with FamilyTreeDNA, a Houston based company that specializes in DNA genealogical testing, has over two dozen participants with variations of the name, Fankhauser, Fanckhauser, Frankhouser and Funkhouser, from America and Switzerland. All show a close enough relationship that they share a common ancestor who lived at Fankhaus in the Emmenthal Valley of Canton Bern, Switzerland within the last 400 years. Several Swiss lines of the family can be traced back with confidence to fifteenth century ancestors in Fankhaus, and a Frankhouser family with roots in colonial Pennsylvania is descendant from two immigrant brothers, who were born in Alsace, but can be traced back to the Emmenthal Valley of Canton Bern, Switzerland. There is no such paper trail for the three Fankhauser (Funkhouser) pioneers in Virginia.
So while it can be said with confidence that Johannes Fanckhauser (John Funkhouser Sr.), has roots in the Emmenthal Valley of Bern, the existing family trees showing direct links to any specific Swiss ancestors are based on erroneous, and in some cases, totally fabricated information.
What is known is that Johannes Fankhauser arrived in Philadelphia, August 23, 1728, aboard the ship "Mortonhouse" and signed the oath of allegiance as Johannes Fanckhauser, the next day, in a distinctive German cursive. There is a nine year gap before there is another known record of Johannes Fanckhauser. On July 23, 1737 a group of men who had recently arrived in the Shenandoah Valley signed a petition to the Orange County Court, objecting to the route chosen for a road they were required to help open. Among the fifty-one men who signed were; Johannes Fanckhauser, Jacob Fanckhauser and Christian Fanckhauser.
Johannes Fanckhauser established his home on the headwaters of the south branch of Tumbling Run and was well settled there before Lord Fairfax opened his office to survey and grant patents to the settlers in 1748. John applied for a warrant and had 400 acres surveyed "where he lived and had made improvements" April 27, 1750. He received the patent for it, January 9, 1752. The following month he applied for another warrant and had an additional 294 acres surveyed. He received patent for that tract, December 28, 1762. A record of John Funkhouser's naturalization has not been found but his name appears on a list of Frederick County citizens who voted for George Washington for the House of Burgesses in July 1758.
John Funkhouser came to "troublesome and dangerous illness" in the winter of 1760 and wrote his will, 17 February 1760. Johann Nicolaus Becker [Baker], Adam Brodbeck and George Hottel witnessed it. He named his wife, "Bebe" [A Swiss diminutive for Barbara], referred to his five sons, but only named his oldest son, John, mentioned an unspecified number of daughters and indicated that some of his children were underage. He signed his will, Hannes Fanckhauser. With exception of the spelling of the first name, it matches closely the signature on the 1728 oath of allegiance and "Hannes" probably comes closer to what he was actually called in his lifetime. "Hannes" apparently recovered and lived several more years and probably died in the winter of 1764-65, since his will was not probated until March 5, 1765. An inventory of property was made April 1, 1765. 
A variety of sources have information on John Funkhouser Sr. The earliest Funkhouser history based primarily on oral traditions was: Jacob Funkhouser, A Historical Sketch of the Funkhouser Family, Harrisonburg, (1902). According to this account John Funkhouser and wife Mary settled in Virginia about 1740 but there is conflicting information about his origins. On one page the author states that they were of Swiss origin and that John and Christopher left Bern Switzerland and settled in Fredericksburg Virginia about 1700 but on another page refers to recollections of Martin Miley, who stated that his great-grandfather, John Funkhouser and wife Mary came from Zurich, Switzerland about 1740. Documentary records have since determined that much was lost or distorted in the oral traditions. It can now be stated with certainty that the Funkhouser (Fankhauser) family originates in the Emmenthal Valley of Canton Bern, Switzerland, John was in Virginia by 1737 and his wife was named Barbara, not Mary. The identity of his parents and specific ties to Swiss ancestors remains a mystery. Reliable sources included Land Grant records, Tax and property records and probate records.
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