ABSTRACT: A more objective classification of ecosystems and their relationship to species diversity could aid the use of ecosystems in conservation planning. The increased availability of environmental data with depth allows more comprehensive modelling of the distribution of marine ecosystems in space, how they relate to species diversity, and can contribute to conservation planning. We provide the first comparison of near surface and seabed ecosystems and their species diversity. We used long-term averages of 17 ocean variables to classify the surface and near-seabed waters in the exceptionally species-rich West Pacific. Twelve distinct 'ecosystems' were identified in each of near-surface and seabed depths, that is enduring regions demarcated by ecologically relevant environmental characteristics. The species assemblages were very different between ecosystems. However, 6 methods of estimating species richness found no simple relationship between ecosystems, nor clear patterns with latitude, depth, area or temperature, reflecting the varying latitude and environmental conditions in each ecosystem. Thus, while ecosystems are part of biodiversity, they cannot be used as surrogates for species richness.