The history of the Department of Biology dates back to the inception of the University in 1876. Henry Newell Martin (B.Sc., M.B. Cambridge, 1873), an associate of Thomas H. Huxley, was the first Professor of Biology. He held this appointment from 1876 to 1893, concentrating much of his efforts on vivisections. To complement his specialty, William Keith Brooks (A.B. Williams, 1870; Ph.D. Harvard, 1875) was appointed associate professor of morphology in 1883, and later promoted to Professor of Zoology. Under these two men a continuing tradition of research was born, whereby faculty and graduate students worked together.

The founding of the Johns Hopkins Medical School in 1893 caused a reorganization of the Biology Department. In 1902 the study of biological sciences was delegated to the Medical School, while Zoology, Botany, and Animal Physiology remained with the Faculty of Arts and Sciences. By 1909 the Animal Physiology courses, designed to meet the needs of medical school students, were being conducted in the Medical School Laboratories, and in 1917 they disappeared entirely from the undergraduate curriculum.

Meanwhile, instruction and research in zoology and botany continued to expand. Duncan Starr Johnson (B.S. Wesleyan University, 1892; Ph.D. Johns Hopkins University, 1897) was appointed Professor of Botany in 1906. Through Johnson's efforts, the Botanic Laboratory and Gardens were created; he directed them until his death in 1937. As director of the Laboratory and Gardens Johnson travelled throughout the world (including seven trips to Jamaica alone), collecting flora and fauna.

A new area of study, Plant Physiology, was established in 1909 under Burton E. Livingston (A.B. University of Michigan, 1898; Ph.D. University of Chicago, 1902). He served for thirty-one years as Professor of Plant Physiology and Director of the Laboratory of Plant Physiology at Hopkins, until his retirement in 1940. In 1925, he was named to the post of Permanent Secretary of the American Association for the Advancement of Sciences, which he retained until his death in 1948. In 1913, Zoology, Botany and Plant Physiology were listed in the Annual Report as one department for the first time.

Due to the presence of such scholars as Martin, Brooks, Johnson and Livingston, Biology attracted a great deal of attention to the University. Enrollment growth was tremendous after World War One, resulting in the division of the first-year biology class into two sections in 1920. So great was the interest in biology that an Institute for Biological Studies, designed to research all aspects of general biology, was created in 1925. Unfortunately, the Institute was in existence for only four years, until 1929.

The new Biology Building, Mergenthaler Hall, was completed for the 1940-1941 academic year, and the department assumed the name Biology Department, replacing the component parts Zoology, Botany and Plant Physiology, under which the department had been known. Benjamin H. Willier (B.S. Wooster College, 1915; Ph.D. University of Chicago, 1920) chaired the department from 1940 until 1955, and he also held the Henry Walters Chair of Zoology from 1940 to 1958, when he retired and was named Professor Emeritus. Willier was the catalyst for many new developments within the Biology Department, notably the creation of the Thomas C. Jenkins Department of Biophysics in 1946, and the Chesapeake Bay Institute in 1947. In 1945, Willier was elected to the National Academy of Sciences.

Upon Willier's retirement from the Biology chairmanship in 1955, William D. McElroy (B.A. Stanford University, 1939; M.A. Reed College, 1941; Ph.D. Princeton University, 1943) was named to the position, where he served until his 1969 appointment by President Richard Nixon as Director of the National Science Foundation. McElroy joined the Hopkins faculty in 1946 and became Professor in 1950. He served as Director of the newly formed McCollum-Pratt Institute, which is devoted to the study of micronutrients, from 1948 until 1968. McElroy became a celebrity while carrying out his famous firefly experiments, which won him numerous awards and recognition.

Saul Roseman succeeded McElroy as Chairman of the Department and Director of the McCollum-Pratt Institute in 1969, holding both appointments until 1972. During this time, the Department of Biomedical Engineering became an independent department. William Harrington (B.S. City College of New York, 1941; Ph.D. University of Wisconsin, 1948), a Johns Hopkins faculty member since 1965, became chair of the department and Director of McCollum-Pratt in 1973. In 1983, Dennis Powers succeeded Harrington in both positions.