Pilsbry soon proved capable of prodigious efforts, and his scientific output was remarkable. During the next five years he produced hundreds of detailed pages of the "Manual of Conchology", preparing many of the plates himself, and founded "The Nautilus", an influential journal of malacology which has survived into the 21st century. He also married during this period, to Adeline Avery. His college, the University of Iowa, honored him with a Doctor of Science degree in 1899 (and he later received two other honorary doctorates: University of Pennsylvania, 1940, and Temple University, 1941). In 1929 he participated in the Pinchot South Sea Expedition. Pilsbry was the first president of the American Malacological Union (Society) founded in 1931.