Bean is probably best known for the work in systematic ichthyology that he did while in Washington, particularly in collaboration with Goode. The pair wrote 39 papers together, culminating in "Oceanic Ichthyology" (1896). They were the beneficiaries of the extensive survey and collecting activities being done by Fish Commission vessels in the poorly explored deep waters off the coast of North America. Bean was also an authority on the fishes of Pennsylvania, New York, Bermuda, and Alaska. Most of his later papers dealt with fish culture, and at the time of his death he was considered the nation's premier authority on that subject. He was also a dedicated educator, from his early teaching days in Pennsylvania to his work on the great international exhibitions and his many popular articles and lectures on fishes, forestry, and conservation. Bean was a pioneer in the growth of American ichthyology in the post-Civil War years and by the end of his life was one of its most respected and honored members.