(classes Leptocardi, Myxini, Petromyzonti, Elasmobranchii, Holocephali, Cladistii, Actinopteri, Coelacanthi and Dipneusti)

There are an estimated 34,500 lot of specimens representing at least 3,828 species, with type material for at least 550 nominal species. Most of the specimens are kept whole in liquid preservatives, while a small number are stuffed and dried.

Fishes from freshwater and marine localities in Southeast Asia (including Singapore) from the 1950s to the present day by museum staff and collaborators from regional scientific institutions form a large part of the fish collection. Many specimens from Southeast Asia and beyond were also sourced from the food fish trade and ornamental fish trade in Singapore. 

Of historical interest are a collection of fishes from the inland waterways of Singapore Island in the 1960s before these drainages were dammed and cut off from the sea. A few of the freshwater species (such as the catfish Glyptothorax fuscus and the eel-loach Pangio semicincta) and are believed to have become locally extinct today. There is also a collection of fishes trawled from the South China Sea and Andaman Sea in the 1950s and 1970s contributed by the Southeast Asian Fisheries Development Centre (SEAFDEC).