Boethius was the third son of Hezekiah Pendergast. He had three brothers, Antoine, Comstock, and Maurice. He had two sons (Ambergris and Pendergast's so-far-unnamed grandfather) and a daughter, Cornelia.
Boethius was a personal friend of the American painter John James Audubon. His grandfather was an early patron of Audubon's work and the family still owns many priceless Audubon folios, which are currently housed at the family's country estate, Penumbra. Aloysius Pendergast's late wife Helen's obsession with Audubon was central t the plot of the tenth Pendergast novel, Fever Dream.