The Center for Quantitative Fisheries Ecology was conceived by Dr. Cynthia Jones in the 1998 based on her work with the Virginia Marine Resource Commission evaluating fish populations in Chesapeake Bay.

In 2006 CQFE obtained its own building on the campus of Old Dominion University. The building has offices for resident and visiting researchers from around the world, post doctoral fellows and graduate students studying with Dr. Jones, labs for extracting and preparing hard parts (otoliths, scales, opercula, spines),  microscopy labs for hard part analysis, and a Class 100 clean room.