On 7 June 1904, Frederick Francis married Princess Alexandra of Hanover in Gmunden. She was the second eldest daughter of Ernest Augustus, Crown Prince of Hanover, and his wife, Princess Thyra of Denmark, a daughter of King Christian IX.
Alexandra and Frederick Francis had five children:
Friedrich Franz, Hereditary Grand Duke of Mecklenburg-Schwerin (22 April 1910 – 31 July 2001). Married Karin Elisabeth von Schaper, daughter of Walter von Schaper and his wife Baroness Louise von Münchhausen. The couple had no issue.
Duke Christian Louis of Mecklenburg (29 September 1912– 18 July 1996). Married Princess Barbara of Prussia, daughter of Prince Sigismund of Prussia and Princess Charlotte of Saxe-Altenburg.[2] The couple had issue.
Duchess Olga of Mecklenburg-Schwerin (1916–1917).
Duchess Thyra of Mecklenburg-Schwerin (18 June 1919 – 27 September 1981).
Duchess Anastasia of Mecklenburg-Schwerin (1922 – 1979). Married Prince Friedrich Ferdinand of Schleswig-Holstein-Sonderburg-Glücksburg, son of Prince Albrecht of Schleswig-Holstein-Sonderburg-Glücksburg and Countess Ortrud of Ysenburg and Büdingen. The couple had issue.