Coral reefs offer settling fish larvae a spatial mosaic of microhabitats that differ not only in structural complexity but also in the abundance and diversity of predators. This paper provides evidence that interactions between predators and prey are causally linked to variation in relevant architectural characteristics of natural substrates. Juvenile bicolor damselfish, Stegastes partitus, experienced greater mortality on Montastrea annularis boulder coral than on piles of Porites porites coral rubble. This pattern was consistent on both back and fore reef habitats. Architectural differences, variable encounter rates with predators, and access to different food sources all contributed to higher mortality. Spatial and structural differences among refuges provided by the two substrates were most important in affecting survival. Porites rubble contained almost three times the number of crevices (39.9 vs. 14.3 crevices m(-2)), had a much smaller mean crevice size (15.9 vs. 48.5 cm(2)), and had a more complex internal structure than Montastrea coral. Survival of juvenile fish living on Montastrea coral was positively correlated with crevice density (r(2) = 0.41) whereas survival of fish living on Porites rubble was negatively correlated with crevice size (r(2) = 0.43). These patterns were evident on fore reef habitats only, whereas on back reef habitats no clear patterns emerged. The effect of these natural differences in architecture on mortality rates of juvenile S. partitus was experimentally tested in the field using a combination of natural and artificial substrates. As the number of large shelters was increased I found that the density of potential predators increased but the survival rates of juvenile bicolor damselfish declined. These results highlight the importance of structural architecture among common reef substrates in affecting predator-prey relationships and in determining the survivorship and small-scale distribution patterns of juvenile reef fish.