In October, 1833, when he was twenty-six, Louis Agassiz married Cecile Braun of Carlsruhe, the sister of his life-long friend Alexander. They began housekeeping in a small apartment at Neuchatel, both practising the closest economy that the books might be carried on; the "Fresh-Water Fishes," and the "Fossil Fishes." She was a skilful artist, had done much work for her brother in botany, and now helped her young husband in drawing and coloring his fishes.

Louis Agassiz and his wife Cecile Braun Agassiz had three children.

After the death of Cecile (1846), Louis Agassiz married Elizabeth Cabot Cary who later became the first president of Radcliffe College.