Facts and Events
The website Rockaway Records states that John was married to Elizabeth Hallet and to Elizabeth Layman. This info was probably taken from the records of J. Pearcy Crayon, as Mr. Crayon is quoted below saying the same thing. Oscar B. Robbins' book "History of the Jackson Family" pg 3 notes that Elizabeth Layman should be Elizabeth Seaman. This was probably a mis-reading of the old records as old-style handwriting 'S' & 'L' look very similar.
Page 3 of this same Robbin's book quotes J. Percy Crayon who ascribed two wives to Col. John. This error is covered in detail in the Jackson Family Genealogy Table of Contents, click on Conflicting Data. Please read the detail there, but to summarize, Crayon seems to have left out a whole generation. Subsequent study indicates both of these sources are probably in error. Elizabeth Seaman was Col. John's wife and Elizabeth Hallett was the wife on the Colonel's son, John. Col. John's will and the book "Long Island Genealogies" by Bunker greatly helped in resolving this issue and getting these children with their proper parents.
The 1724 Will of Col. John Jackson is available here: Transcript:Will. John Jackson 26 Aug 1724 Heirs are sons Samuel, John, and James, daughters Martha Titus, Elizabeth Doughty, Hannah Seaman, Sarah Barnes, son-in-law Jeremiah Scott and daughter Mary Scott's four daughters. Daughter Mary had died but Col. John provided for her children.
Don Norman's records show John married only to Elizabeth Seaman. Don also records "John was a member of the Assembly in 1664 when the Colony of New York was established. He is recorded as Captain of the Queen's Troops in 1689, as a Juryman in 1691, as High Sheriff 1693-1716, Representative to the Colonial Legislature in 1699, Justice of the Peace in 1700, as Lieutenant Colonel in 1701, as Colonel in December 30, 1701, as a member of the protestant Petition to King William III in 1703, as Commissioner of Highway 1710-1723 and as Judge of Queen's County from 1723 until his death in 1725."
There is a record by William Jackson that is quoted in Oscar Burton Robbins' book "History of the Jackson Family" page 5 that has caused quite a bit of mixup. I am quoting it here with my interpretation of the paragraph: "Colonel John Jackson . . . left three sons and five daughters, viz; first, Samuel, son of Colonel John Jackson, by his father's Will inherited the Homestead, which was situated at Jerusalem in the Town of Hempstead. His children were Richard, Townsend, Thomas, Ruth, Jerimah (sic) m. James Hewlet, Letitia m. Solomon Pool, -Mary m. John Pratt and Martha m. Samuel Birdsall. by William Jackson" The first sentence agrees with children listed in John's Will. But the problem here is that the next sentence listing the children says 'his children' and does not refer to Colonel John but instead refers to the aforementioned Samuel. Richard, Townsend, Thomas, Ruth, Jeremiah, Letitia, Mary and Martha are all children of Samuel and grandchildren of Colonel John.
Family Tree DNA is the laboratory which has the most Jackson samples to compare to. The unique 12 marker haplotype of Group B Hempstead, 15,22,15,10,15,16,11,13,11,14,12,30, immediately separates these members from other Jackson lines. They appear to establish the 67 marker ancestral haplotype of Col. John Jackson the eldest son of Robert Jackson of Hempstead, Long Island, New York. This group has been fortunate in that well documented descendants of John, son of Robert of Hempstead, have come forward to volunteer to participate in DNA testing even though they have good documentation and had no doubt about their ancestors. But they participated so that others without good documentation would have DNA material to compare to and thus verify their relationship to this Jackson line.
Here is a link to the public results page at FTDNA: