Spatial variability in the structure of subtidal macroalgal assemblages in southwest Australia was examined at multiple spatial scales using a three-factor hierarchal design. Spatial extents ranged from metres (between quadrats) to many hundreds of kilometres (between regions), and the study encompassed >2000 km of temperate coastline. In addition, the influence of taxonomic resolution, from species level data through to class level, on spatial patterns was investigated to assess the potential evolutionary timescales of the pattern and for developing cost effective regionally applicable surrogates for biodiversity monitoring. Almost 300 species were identified from 14 sites, representing considerable biodiversity and a significant subset of the total benthic macroalgal diversity in the region (~1000 species). Multivariate variability was significant at all spatial scales examined, but most prominent at smallest spatial scales, regardless of taxonomic resolution. Assemblage and species turnover was pronounced at scales of metres to hundreds of metres. Generally, small scale patchiness was a ubiquitous pattern for all individual taxa examined, regardless of taxonomic resolution, while variability at the scale of 10s km was less important. Even so, differences in spatial variability between taxa were observed, and ecological and historical reasons for such differences are proposed. Taxonomic aggregation to family level had minimal effect on spatial patterns, but aggregation to order level led to changes in some aspects of patterns of assemblage structure. The unique and speciose macroalgal assemblages on subtidal reefs in southwest Australia are shaped by a complex array of historical and contemporary processes that act at multiple spatial (and temporal) scales. Understanding the relative importance of these processes requires that further manipulative and correlative work is conducted across a range of ecologically-important spatial scales.