Jonathan was born January 9, 1656/ 57 at Middletown, Connecticut and married May 11, 1681 to Dorcas Hopkins, daughter of Stephen and Dorcas Bronson Hopkins, and grand-daughter of John and Jane Hopkins, and of John Bronson. Dorcas died in 1695, and Jonathan married Mary Judd, the supposed daughter of Thomas Judd. His brother, Joseph, also married a Mary Judd, daughter of Benjamin Judd.
The children of Jonathan and Dorcas Hopkins Webster were:
Jonathan, born 1682; Samuel; Susannah, 1686; Mary, born 1688; Mehitable, born 1691; Stephen, born 1693.
The child of Jonathan and Mary Judd was Benjamin born August, 1698.
His children, in 1735, are mentioned as Susannah Steele, Mary Brace, Mehitabel Bidwell, Benjamin, and the heirs of Stephen and Jonathan, but Samuel is not mentioned.