In 1987, Daniel Pauly, inspired by cataloging work of Walter Fischer for the FAO in the 1970s, proposed a standardized database for fish species, originally calling it the "ICLARM Software Project". The following year he began to work with Rainer Froese, who had been working on an expert system to identify fish larvae. After an abortive attempt to build a system using PROLOG, Froese switched to DataEase, a relational database for MS-DOS. In 1989 the project received its first grant.
In 1993 the project switched to Microsoft Access, and 1995 the first CD-ROM was released as "FishBase 100". Its initial reviews in scientific journals admired the scope but criticized the many gaps in coverage. Subsequent CD releases have come annually, with the FishBase 2000 release needing four CDs.
As awareness of FishBase has grown among fish specialists, it has attracted several hundred contributors and collaborators. In order to preserve its value as a scientific database, FishBase is not allowed to include original data; all of its content must be based on previously-published material.