Previous studies describing Western Australian marine fish fauna have been either (1) broad-scale biogeographical descriptions or (2) considered smaller spatial extents and assessed the influence of local habitat variation on fish assemblage structure. This study simultaneously considered the relative effects of geographical distance and environment in structuring the Western Australian ichthyofaunal assemblages across spatial scales. Abundances of 440 species were estimated from baited underwater video sampling. Kruskal-Wallis tests were used to test for changes in species richness among locations. Changes in community composition relating to environmental and spatial gradients were analysed using multivariate regression trees. Species richness displayed a non-monotonic decrease along the expected north-south geographical gradient. At the broadest scale, 2 distinct assemblages were detected, the Indo-Pacific tropical ichthyofauna and a temperate assemblage with varying degrees of local endemism. Space was the greatest influence on the structure of fish assemblages in tropical localities, but local habitat properties were more important in temperate locations. At the biogeographic scale, in Western Australia, the elsewhere widespread Indo-Pacific ichthyofauna has a restricted distribution, while temperate species have greater geographical ranges. This difference may be attributed to the greater environmental heterogeneity seen among tropical locations in this study, creating less continuous suitable habitat for species. Within locations, habitat was found to be the greatest driver of assemblage structure, suggesting the importance of habitat filtering as a process structuring ichthyofaunal assemblages at smaller spatial scales.