This is another area where there is confusion. He had THREE wives. He married Mary Heath, daughter of William Heath and Agnes Cheney. Mary Heath died prior to May 15, 1629 and was buried on May 15, 1629 in the cemetery surrounding St. Mary the Virgin Church in Ware, Hertfordshire, England. John Johnson's six surviving children were all children with Mary Heath.
John Johnson married second, Margery, perhaps in England, just prior to immigrating to America in 1630. They did not have any children. Margery's parents are unknown. She was buried in Roxbury, MA in the First Burying Place now called, Eliot Burying Ground near the First Church of Roxbury on April 9, 1655. If you want to read the discussion on WHY this Margery was not Margery Scudder, read Gerald Garth Johnson's book (see the project for the complete reference).
John Johnson married third, Grace Negus Fawer, a widow of Barnabus Fawer of Dorchester, MA. I have seen another given name for Grace Negus Fawer's husband. Grace Fawer had a child with her first husband who died before her marriage to John Johnson. Their marriage may have taken place prior to October 14, 1656. They had no children. Grace Negus Fewer Johnson died December 19, 1671.