For many regions worldwide, multiple and often contrasting biogeographic classifications exist that are derived from a variety of taxa and techniques. This presents a challenge for managers who must choose appropriate large-scale spatial frameworks for systematic conservation planning. We demonstrate how systematically collected community data can be used to evaluate existing biogeographic classifications, identify the most appropriate metric for biogeographic patterns seen in other taxonomic groups, and develop an independent biogeographic classification scheme for systematic conservation planning. We evaluated 6 existing biogeographic classifications for New Zealand's nearshore marine environment with community-similarity metrics derived from abundance and presence-absence data for macroalgae (107 species) and mobile macroinvertebrates (44 species). The concordance between community metrics and the previous classifications was high, as indicated by a high multivariate classification success (CS) (74.3-98.3%). Subsequently, we carried out an independent classification analysis on each community metric to identify biogeographic units within a hierarchical spatial framework. The classification derived from macroalgal presence-absence data achieved the highest CS and could be used as a mesoscale classification scheme in which 11 regional groupings (i.e., bioregions) (CS = 73.8-84.8%) are nested within northern and southern biogeographic provinces (CS = 90.3-98.7%). These techniques can be used in systematic conservation planning to inform the design of representative and comprehensive networks of marine protected areas through evaluation of the current coverage of marine reserves in each bioregion. Currently, 0.22% of the territorial sea around mainland New Zealand is protected in no-take marine protected areas in which 0-1.5% of each bioregion represented.