John Perry 'appears' in the historical record in Kilboy, Tipperary in around 1760, when he is granted lands in Graystown, Tipperary by his father-in-law, John Hughes, following his marriage to Mary Hughes. No other Perrys are named in the document so there are no clues there as to his origins.
There are other clues however, as to where he came from, but also evidence that appears to contradict these clues. One of the strongest theories is that he is a member of the Perry family of Woodrooff, near Clonmel, Tipperary. Clonmel is only around 20 miles away from Kilboy and seems the likeliest option, especially as many of the first names used in the Kilboy family are similar to those used in the Woodrooff family, a pattern that is often seen in Irish families. Additionally, a biography of John's great grandson, Samuel Perry of Wisconsin, refers to a 'granduncle of Woodrooff', suggesting that there may be a connection between the two families, although the uncle is named incorrectly. However, two members of the Kilboy family have taken part in the Perry DNA test, as has a proven descendant of the Woodrooff family and their Y-dna does not match, which means that there is certainly no common ancestor in the male line
There are numerous theories as to where John Perry originated from. He could have come from the Laois Perrys, the Formerla Perrys or indeed another unexplored branch. However, my opinion is that he is a descendant of the Woodrooff Perrys, albeit not in the male line. It is possible that an unmarried female Perry had a child, inheriting his mother's name, but his father's DNA. Or that a Perry man married a woman who already had children and who took his name, but not his DNA. We may never know the answer and while work goes on in the archives of Ireland by various Perry descendants, we also hope that another researcher's DNA results might one day give us another clue. Although an immense amount of work has already been undertaken on the question of who John's father was, it is worth remembering that our branch of the family had our own brick wall for more than twenty years and that sometimes we can find the missing link when we have completely given up hope!