A dedicated educator who preferred to teach a few research students at a time, he made major contributions in the areas of evolution and embryology of worms, comparative anatomy, heredity, and animal behaviour.

Following graduation, Whitman became principal of the Westford Academy, a small Unitarian-oriented college preparatory school outside Lowell, Massachusetts.

Influenced by his training in Germany, he introduced systematic methods of biological research, including the use of the microscope.After leaving Japan, Whitman performed research at the Naples Zoological Station (1882), became an assistant at the Museum of Comparative Zoology, Harvard University (1883–5), then directed the Allis Lake Laboratory, in Milwaukee (1886–9), where he founded the Journal of Morphology (1887).

[7][8][9] Over the course of his career, Whitman worked with more than 700 species of pigeons, studying the relationship between phenotypic variation and heredity.

By the turn of the 20th century, the last group of passenger pigeons, all descended from the same pair, was kept by Whitman at the University of Chicago.