What is known about the provenance of this John James?
James family researcher and our cousin* Dorothy Louise (née James) Turner (1917), wrote a book about her James ancestral line called The James family, 1600-1979. I have not yet found a copy of this book, but she apparently did not definitively identify the parents of John James (1688). Several online summaries of the book start with this sentence:
"John James was born in 1688 in England, possibly the son of William James of Kent County, England".
A search for a birth record of William James in Kent County provides 10 possibilities (at the time of my search) for Williams James born between 1631 and 1671. Perhaps one of these is the father of our John James. More research is needed.
This "Busy" Family Tree was created in 1980 by James family researcher Jesse Sibert James (1906), brother of Clyde James (1919). It also shows William James as the father of John James. However, no source for this information is provided. Perhaps Jesse Sibert James got this information from cousin Dorothy's aforementioned book.
Many family trees have William James and Ann Wyndham as the parents of John James. This information is likely based on the book Selden and Kindred of Virginia which states "John James, born 1688, was the son of William James, born 1658, who married Anne Wyndham." There is no source citation for this information, and it appears to be incorrect.
The marriage of William James and Anne Wyndham was in June 1697, eight years after the birth of our John James (~1688). So, either his birth year is incorrect or these two cannot be his parents. Also, our John James married Justina Thruston in 1712, so he must have been born before 1697.
Conclusion: William James and Anne Wyndham were not the parents of our John James.
Marriage of William James and Ann Windham, London, England
Wimborne Minster, Dorset County, England
In the registers of Wimborne Minster, Dorset County, England, there is a baptismal entry for a John James, son of William, born on May 23, 1688.
Bristol, England
A search of Bristol archives yielded a birth record for a John James, born August 17, 1688, in Bristol. The father on this birth record is listed as Henry James.
We know that our John James married Justina Thruston in Bristol, so finding a John James that was born in Bristol is an intriguing possibility.
Searching Bristol archives for a marriage record of a Henry James resulted in a hit. Henry James married Mary Beratt on April 16, 1686.
Searching Bristol archives for a birth or baptismal record of Henry James resulted in a hit. Henry James, son of Thomas James, was born on April 3, 1643.
All of this is circumstantial. Our John James, husband of Justina Thruston, could be either of these two, or neither. Since the marriage record of John and Justina does not identify their parents, we are not likely to find a definitive answer. As of now, this is a genealogical brick wall.
DNA testing could provide a breakthrough. A Y-DNA test from a male James descendant would be ideal. It has to be a male descendant whose father is also a James, since Y-DNA is passed only from father to son.