Host specificity data for gnathiid isopods are scarce because the parasitic stages are difficult to identify and host-parasite contact is often brief. We examined two common nocturnal species, Gnathia falcipenis and Gnathia sp. C, collected in light traps from two locations at Lizard Island on the Great Barrier Reef, Australia. Engorged third stage gnathiids were photographed and permitted to moult into adults to allow identification. We compared approximately 580 bp sequences of 16S mtDNA from blood meals with host sequences available on GenBank using BLASTn. Where homology was <98%, familial identity was investigated with neighbour-joining trees. All blood meal sequences (n=60) and homologous fish sequences (n=87) from GenBank were used in a Bayesian analysis, which identified all but three sequences to family. The host frequency distributions used by each species were significantly different; only four host families were shared. No gnathiids fed on elasmobranchs, blennies or apogonids, and most fed on host families whose representatives are typically large. Gnathia sp. C showed a distinct predilection for nemipterids. Gnathia falcipenis often parasitised sand-dwelling families, and unlike sympatric diurnal gnathiid species, it also frequently parasitised pomacentrids. We conclude that G. falcipenis and Gnathia sp. C operate as generalist micropredators with preferences.