Artificial reefs, a common management tool for stock enhancement of recreational fisheries and marine habitat restoration, have been deployed all over the world. However, little is known about the attractiveness of artificial compared to natural reefs to reef fishes. Here we investigated the habitat preferences of three reef fish species: Trachinops caudimaculatus, Vincentia conspersa and Trinorfoklia clarkei through the observation of recruitment patterns to three study habitats: Reef Ball reefs, custom-designed artificial reefs, and natural reefs in Port Phillip Bay, Victoria, Australia. Additionally, we examined habitat preferences of new recruits of T. caudimaculatus and V. conspersa using laboratory-based habitat choice experiments. In general, T. caudimaculatus recruitment was at least twice as high on natural reefs compared to both artificial reefs, whereas V. conspersa recruitment was almost three times greater on Reef Ball reefs compared to the other two habitats. T. clarkei recruited in equal numbers across all habitats. However, in the laboratory experiments T. caudimaculatus recruits selected the Reef Ball reef almost three times as often as the other two habitats, while V. conspersa exhibited no habitat preference. Little is known about the growth, condition, survival or reproduction of individuals that occupy artificial reefs. In areas where habitat is not limiting, the higher preference or equal attractiveness of some artificial habitats may negatively influence fish populations, if larvae are redirected to poorer quality artificial reef habitat, that lead to lower fitness advantages.