A unique opportunity to compare the structure of soft-bottom macrofaunal communities to environmental sediment characteristics arose during a multi-agency sampling survey in Santa Monica Bay. Macrofaunal species, sediment chemistry, highly partitioned sediment granulometry, and depth inventoried at 24 sites, were extensively analyzed to determine community relationships, natural species distributions, and response to anthropogenically derived sediment variables. By employing parsimony analysis, specifically a derived variant of parsimony analysis of endemicity utilizing step-matrices to accommodate species abundance, and multivariate methodologies launched from the branch-length distance matrix derived from the cladogram, community structure was assessed based on the hierarchical or nested spatial relationships of the species and sample areas. Since spatial autocorrelation is implied by the cladistic and hierarchical relationships of the sample localities, and because hierarchically related objects do not comprise independent nor identically distributed data points, the novel application of independent contrasts (correcting for the nonindependence of the data distributed on the cladogram) was used in combination with traditional statistical methods (that assume observation independence). Both approaches revealed moderate to strong correlations of several abiotic factors with community structure, and between the various phylodiversity and response indices to numerical effects-based sediment quality guidelines. Specifically, community relationships were correlated with depth, polychlorinated biphenyl, several clay-mineral species, and certain sediment phi size bins. Phylodiversity indices correlated more highly with sediment quality guidelines than did the benthic response index.