The temperate waters around Australia's southern coast possess a unique fauna. Distinct from that of the tropics, it was also radically different from that of the northern hemisphere familiar to Frederick McCoy before his arrival in Melbourne. It is therefore unsurprising that 61 fish were included in the Prodromus, making it the second largest group featured.

From an estimated 600 species of fish inhabiting Victorian waters, McCoy's choices of which to illustrate were governed by opportunity, size and an eye to the market. Many were taken from the closest saltwater environment, Hobson's Bay, while other interesting specimens were provided by Mr. Jenkins, a Melbourne fishmonger with whom McCoy seemed to develop a particular rapport.

Of the few freshwater fish illustrated, McCoy focused on larger species with commercial value, such as the Golden Perch and Murray Cod. Spectacular or dangerous fish were also well covered, with 14 species of sharks, along with oddities such as the Tasselled Anglerfish and deep sea Oarfish.

McCoy planned to provide a much more systematic coverage of Victorian fish, particularly species with commercial potential, and of the 84 unpublished plates 40 were dedicated to fish. These included individual plates for juvenile, female and male Snapper, as well as John Dory and Boarfish.

An impressive suite of drawings was also retained in the collection, almost all by Arthur Bartholomew. Created with the intent to publish, these contain all the information required to complete a lithograph in the style established by the Prodromus. Bartholomew's concentration and meticulous eye for detail made his original fish drawings more compelling and lively than many completed prints.