He married Frances Cromwell . Frances Cromwell was born at of Hinchingbrooke, Huntingdonshire, England 1589 daughter of Henry Cromwell and Joan Warren .
They were the parents of 6
children:
Thomas Whalley
born Abt 1611.
Elizabeth Whalley
born Abt 1613.
Edward Whalley
born Abt 1615.
Robert (Theophilus) Whaley
born 1616.
Henry Whalley
born Abt 1617.
Jane Whalley
born Abt 1618.