The Ichthyology Department is housed in the Museum of Comparative Zoology Laboratories and in the historic Museum of Comparative Zoology (MCZ) building with its research collections. The MCZ is associated with Harvard University's Department of Organismic and Evolutionary Biology (OEB) under the Faculty of Arts and Science (FAS).

Ichthyology has been studied at Harvard since long before the founding of the Museum of Comparative Zoology (MCZ). By the late 1700s, William Dandridge Peck, the first professor of Natural History at Harvard, had collected and published on New England fishes. Peck's specimens were skinned, dried and glued to paper sheets; some are still in the MCZ collection to this day. After the MCZ was founded by Louis Agassiz, the fish collection grew rapidly and has had a long history of active ichthyological research. Over the last 20 years, one of the primary projects has been developing the MCZ's Atlantic deep-sea fish collection in collaboration with colleagues at the Woods Hole Oceanographic Institution (WHOI).

Today, the MCZ Ichthyological Collection remains one of the best in the world and emphasis is placed on teaching with very active undergraduate and graduate student research programs. The Fish Collection has been fully renovated and its holdings are available on World Wide Web. The collection's holdings are almost 167600 lots with over 1.5 million specimens as of January 2007.