In 1328 Bernhard married Agnes (c. 1310 – 4 January 1338), daughter of
Rudolph I, Elector of Saxony and Duke of Saxe-Wittenberg. Her paternal grandmother and namesake
Agnes of Habsburg was a daughter of
Rudolph I, King of the Romans. The spouses were third cousins: Agnes's great-grandfather
Albert I, Duke of Saxony, was a brother of
Henry I, Count of Anhalt, Bernhard's great-grandfather. Bernhard and Agnes had five children: •
Bernhard IV, Prince of Anhalt-Bernburg (died 28 June 1354) • Katharina (c. 1330 – 30 January 1390), first married on 6 October 1356 to
Magnus II, Duke of Brunswick-Lüneburg, then secondly on 11 May 1374 to
Albert of Saxe-Wittenberg, Duke of Lüneburg •
Henry IV, Prince of Anhalt-Bernburg (died 7 July 1374) • Albert (died 1 August 1336) • Sophie (died 18 December 1362), married on 12 March 1346 to
William II, Duke of Brunswick-Lüneburg. In 1339 Bernhard married for a second time to Matilda (died c. 1342), daughter of
Albert I, Prince of Anhalt-Zerbst. Bernhard was more closely related to his bride, being a
second cousin: Matilda's grandfather was
Siegfried I, Prince of Anhalt-Zerbst, younger brother of
Bernhard I, Prince of Anhalt-Bernburg, Bernhard's grandfather. The marriage was childless. In c. 1343, Bernhard married for a third time to another Matilda (died after 28 June 1354), daughter of
Magnus I, Duke of Brunswick-Göttingen. Through her mother Sophie of Brandenburg, Matilda was a great-great-great-granddaughter of
Otto I, Margrave of Brandenburg, older brother of
Bernhard, Count of Anhalt, Bernhard's great-great-grandfather. Bernhard and Matilda of Brunswick-Göttingen had two children: •
Otto III, Prince of Anhalt-Bernburg (died 27 February 1404) • Gertrude, married before 12 August 1371 to Günther XII,
Count of Schwarzburg.