Isak Mogendorff was the son of Jesaja Mogendorff and Gezina Maria Koopmans. He got married to Grietje Trijbits, who died in 1891. The couple had two children: Jacques Isaac and Abraham.
In 1893 Isak Mogendorff got married Henriette de Jong. From this marriage two children were born: Heiman and Grietje. Henriette de Jong died in 1931.
After the bombing of Rotterdam, in May 1940, Isak Mogendorff moved in with the family of his son Abraham Mogendorff.
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Isak Mogendorff died on 28 October 1943 in Westerbork transit camp en he was cremated on 29 October 1943. The urn with ashes was placed on the jewish cemetry Toepad in Rotterdam on the parnasrule, row 3, grave number 25b
Register van joden die in het kamp Westerbork zijn gecremeerd, 1943-1944; archief van de gemeente Westerbork, opgenomen in het archief van de gemeente Midden-Drenthe te Beilen, inv. n 3789