Spatial variation of populations and their assemblages is an important component of many aspects of ecology, including the maintenance of species diversity. In nature, organisms are generally aggregated in patches or form gradients or other spatially related patterns. This investigation quantified the degree of spatial structure in benthic invertebrate assemblages. It examined the distribution of infaunal assemblages of different size, mobility and contrasting life-history strategies (i.e. meiofaunal nematodes and macrofaunal polychaetes) in two offshore muddy habitats in the Celtic Deep and the NW Irish Sea off the west coast of the United Kingdom. The more heterogeneous habitat in the NW Irish Sea was characterised by higher tidal stress and bottom temperature while greater water depth, mean particle diameter and organic carbon content was typical for the comparatively homogeneous environment in the Celtic Deep. In both habitats, the environmental conditions became increasingly dissimilar with separation. A total of 125 nematode and 88 polychaete species were recorded with 69% of the nematode and 49% of polychaete species present at both study sites. Occurrence frequency of species, species diversity and average similarity of assemblage composition was higher in the Celtic Deep than in the NW Irish Sea. Results from correlation analyses revealed statistically robust relationships of community similarity and sample distance. Given their small size and low mobility, nematodes were more susceptible to within-habitat physical variability than larger-sized, more mobile polychaetes. This, coupled with limits to long-distance dispersal and likely restrictions in gene flow, resulted in a significant decrease in community similarity with distance at the spatial scales sampled (i.e. within 0.1-23 km). Polychaetes, in contrast, combined a higher dispersal potential (>23 km) with a relatively high tolerance to within-habitat environmental variability and these were the most likely causes for non-significant relationships between the similarity of their assemblages and sample distance. The potential mechanisms causing the observed variation and implications of results for environmental management strategies are discussed.