The Marine Ecoregions of the World system separates the oceans into 232 ecoregions based on coastal and shelfwater species distributions. We tested the separation of those ecoregions and delineated subecoregions within Western Australian waters using intertidal macroalgal and epiphytic polychaete distributions. Environmental predictors of those assemblages were also determined. We collected macroalgae and polychaetes on 38 rocky intertidal shores within four marine ecoregions from 18°S to 34°S: (1) Exmouth to Broome, (2) Ningaloo, (3) Houtman, and (4) Leeuwin. We evaluated differences in species composition of macroalgae and polychaetes among those ecoregions using pairwise permutational multivariate analysis of variance and delineated subecoregions within each ecoregion using hierarchical cluster analysis. Multivariate relationships between environmental variables and assemblages were determined using distance-based linear models. The species composition of macroalgae and polychaetes significantly differed among ecoregions, with dissimilarity of 78-96% for macroalgae and 62-75% for polychaetes. We identified three subecoregions within Exmouth to Broome and Ningaloo and two subecoregions within Houtman and Leeuwin based on macroalgal distribution. We also found two subecoregions within Houtman and no subecoregion within Exmouth to Broome, Ningaloo, and Leeuwin based on polychaete distribution. Environmental predictors could explain 51% of the total variation of macroalgae and 41% of the total variation of polychaetes. The top two predictors explaining a high proportion of assemblage distribution were sea surface temperature (15% for macroalgae and 12% for polychaetes) and tidal amplitude (10% for macroalgae and 6% for polychaetes). These ecoregions and subecoregions can be used as an alternative spatial framework for classifying rocky intertidal habitats for designing marine protected area networks within Western Australian waters.