The effect of mesh size and diel variability in fish trap catch was investigated on the central Great Barrier Reef in order to select an optimal mesh size for ecological studies of lutjanids (snappers) and lethrinids (emperors). Four mesh sizes, 12.5 mm square, 30 mm hexagonal, 40 mm hexagonal and 50 mm hexagonal were examined over two sampling periods (day versus night) yielding a total of 1571 fish representing 70 species from 451 trap hauls. Mesh size had no significant effect on the total catch rate of fish traps. The 40 mm hexagonal mesh size was, however, the preferred mesh size because the size range of target species ( Lutjanus and Lethrinus) caught in this mesh was greater than that in the 50 mm hexagonal mesh and the mean catch rate tended to be greater than the 30 mm hexagonal mesh. The mean catch rate in the 12.5 mm square mesh was low relative to the mean catch rates of the other mesh sizes tested and the size range of target species caught in the mesh size were not significantly different from that caught in the 30 mm hexagonal mesh. Diel sampling period had a significant effect on the catch of fish traps. More fish were captured at night, with the lutjanids (78% of total catch) and lethrinids dominating night and day catches, respectively. Mesh selectivity in fish traps was probably not a simple function of the ability of a given mesh aperture to retain individuals of a certain body depth. The behaviour and activity patterns of reef fish in response to the visual outline of the traps was considered of prime importance in the mesh selectivity.