Joel Asaph Allen (July 19, 1838 – August 29, 1921) was an American zoologist and ornithologist, born in Springfield, MA.

He studied at Harvard University under Louis Agassiz. He participated in the latter's 1865 expedition to Brazil (in search of evidence of an ice age there, which Agassiz later claimed to have found) and in several others within the United States.

In 1872 he was named assistant in ornithology to the Museum of Comparative Zoology at Harvard.

In 1873 he was the head of the naturalists of the Northern Pacific Railroad expedition from Bismarck, North Dakota, to the Yellowstone and back for the Smithsonian. Florida was another area he explored from a zoological perspective.

With Elliott Coues and William Brewster he in August of 1883 sent the letter inviting selected individuals to form the American Ornithological Union at a meeting to be held in September. He was unavoidably absent from this initial meeting, but was nonetheless elected the new organization's first president.

Allen was the first curator of birds and mammals at the American Museum of Natural History (from 1885 on) and later the first head of its Department of Ornithology.

In 1886, he was one of the incorporators of the first Audubon Society, New York. He was also a member of the American Association for the Advancement of Science, and of the American Philosophical Society. From 1883 to 1886 he was the first president of the American Ornithologists' Union, which he had helped found himself.

The hundreds of letters which Coues (pronounced "cows") sent to him over many decades form one of the cornerstones of the history of American ornithology. Allen famously memorialized Coues in the pages of The Auk, the A.O.U.'s journal, after the latter's death in 1899.

Allen's rule, stating a correlation between body shape and climate, was formulated by him in 1877.

In addition to a great number of scientific papers, he is author of Mammals and Winter Birds of Eastern Florida, (1871); The American Bisons, (1876); Monographs of North American Rodentia (with Elliott Coues, 1877); History of North American Pinnipedia, (1880); Mammals of Patagonia, (1905); Te Influence of Physical Conditions in the Genesis of Species, (1905); Ontogenetic and Other Variations in Musk-Oxen (1913).