Cases of gnathostomiasis, an infection caused by consuming infected seafood, have been reported in Australia. However, doubt exists over the validity of these diagnoses as there are no reports of Gnathostoma spp. in Australian teleost fish. Also, the diagnoses in human cases were based on a serological test developed in Thailand. The specificity and sensitivity of this test in non-endemic areas are uncertain. Interestingly, parasites belonging to the genus Echinocephalus, which morphologically are very similar to Gnathostomum, are commonly found in Australian fish and shellfish and can potentially infect humans. The aim of this study was to determine the occurrence of these zoonotic nematodes within commercial fish and to characterise nematode larvae in order to provide insights into the specific identity of the potential causative agents of gnathostomiasis in Australia. Six edible fish species (n = 163) were examined. Gnathostomid-type larvae were found only in Acanthopagrus australis and Rhabdosargus sarba. Detailed examination and sequence data suggested parasite larvae belonged to the genus Echinocephalus. Further investigation of the occurrence of zoonotic nematodes within marine environments and observation of their spatial and temporal patterns will help raise awareness of the significance of this food safety issue within global fishing industries and health sectors. The accurate identification of zoonotic nematodes is a key component of disease surveillance and control. This information can also be used to develop specific and sensitive diagnostic test.