His father, John Ogden (b. 1609; d. May 1682, Elizabethtown, [present-day Union County], New Jersey, British Colony, was probably born in Lancastershire, England.

Based on research done by John Ogden (1609-1682) biographer, Jack Harpster ["John Ogden, The Pilgrim (1609-1682)," Cranbury, N.J.: Fairleigh Dickenson Press. 2006, (pages 193-195), Jonathan was most likely born after his parents arrived in the American colonies. He may have been born at present-day Southampton, Long Island, which was part of the British colony of Connecticut at the time. Contrary, and most likely incorrect, information on Jonathan Ogden was published in the 1907 William Ogden Wheeler publication, "The Ogden Family in America."

Note: When Jonathan Ogden (Senior) passed away, Julian calendar dates were in use. In 1752, British calendar dating changed, by law, from the Julian calendar to the Gregorian calendar, as a means to correct an error of an additional 1 day every 128 years. The British Calendar Act of 1751, declared the day after Wednesday, September 2, 1752 would be Thursday, September 14, 1752. Therefore, the Julian calendar date of January 3, 1732 is equivalent to January 12, 1732 in the present-day Gregorian calendar.

When Jonathan Ogden (Senior) passed away, New Jersey was still a British Colony, and Union County did not exist. Therefore his correct death location is: Elizabethtown (the name for present-day Elizabeth), Essex County, New Jersey, British Colony. Part of what was Essex County became Union County, New Jersey in 1857.

Children of Jonathan Ogden (Senior) and wife Rebecca Wood Ogden, all born in the British colony of New Jersey:
- Son: Jonathan Ogden (2nd), b. about 1676; d. before 731
- Son: Samuel Ogden, b. about 1678; d. about 1715
- Daughter: Rebecca Ogden (sometimes referred to as: Mary), b. about 1684; d. unknown
- Son: Robert Ogden, b. 1687; d. November 20, 1733, age 46
- Daughter: Hannah Ogden, b. about 1682; d. about 1730

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Information posted by the creator of this Find A Grave memorial, Barbara Doxey:

Some of my Farrand "kissing cousins' have Ogden ancestors. I have information supplied by one of these cousins that indicates that Jonathan Ogden, Sr. was the son of John (the Pilgrim) Ogden, Sr. and Jane Bond and that he married Rebecca Wood (or Warde) in 1764 possibly at Elizabethtown, New Jersey.

It has come to my attention on Feb. 4, 2007 that my original entry of birth on 11 Jan 1639 does not agree with the age of death on the tombstone (86 years) which was photographed by another person. I have therefore changed the date of birth to 1646. Further checking back indicates that I picked up the incorrect date of birth from Latter Day Saint internet records which means that the place of birth is also in question.

Jonathan Ogden and Rebecca Wood (or Warde) were supposed to have had six children (Jonathan, Samuel, Robert Ogden I (1687 to 1733), Hannah, Rebecca, and Benjamin. Another source says that Jonathan and Rebecca are buried in the churchyard of the First Presbyterian Church of Elizabethtown, New Jersey.

My Farrand "kissing cousins" in New Jersey are descended from Robert Ogden I, Robert Ogden II, and the daughter Mary (b. 1778) of Robert Ogden III and his first wife Sarah Platt. Mary Ogden (b. 1778) married Elias Haines and one of their daughters Elizabeth Ogden Haines (1804 to 3/26/1889) married John Macaulay Nixon (1805 to 2/12/1869). One of their many children was the Rev. George Nixon (1834 to 9/28/1910 who married Mary Isabella Deacon (1840 to 2/21/1937) on 10/9/1867 at Kingston, Canada. Two of their daughters Blanche and later Florence were then married to Henry Carroll Farrand (1872 to 11/10/1946). Henry only had children by Blanche (eight). Florence, whom the children had called Auntie Bo, became their stepmother upon the death of her sister Blanche who died 12/10/1926. It is my understanding that Auntie Bo had done much research on her family roots in New Jersey.