Subtidal meiobenthic samples were collected from sediments within a seagrass bed (Thalassia testudinum) and an adjacent barren sand area in the Florida Keys. Fine-scale differences in sediment and heterogeneity, with respect to sediment grain parameters were analyzed using factor analysis. Sediment heterogeneity was related to meiofaunal distributions. Eighteen meiofaunal taxa representing 15 phyla were found. Nematodes comprised 58% of the total meiofauna. Eight gastrotrich, 26 harpacticoid, and one cyclopoid species were found. In comparing the seagrass area to the barren sand area by ANOVA, significant differences in density were noted for total meiofauna and polychaetes, but not for any other major taxa. The gastrotrich, Mesodasys laticaudatus and the harpacticoids Scottolana canadensis, Peltidium sp. and Cletodes sp. A showed significant differences with depth, area, and in the interaction of depth and area. Most harpacticoid species, nematodes, gastrotrichs and turbellaria showed their highest mean densities in the barren area. Polychaetes were most abundant in the seagrass area. Sediments were coarser at all depths in the barren area than in the seagrass area.Using factor analysis, sediments were classified into five sediment types. Stepwise linear regression of species abundance data on sediment types indicated that four of the sediment types were related to the distribution of two gastrotrich and three harpacticoid species (P < 0.01). Relationships of species with specific sediment types are discussed. For examining within-habitat differences in granulometry, factor analysis has provided sufficient resolution to examine the effects of fine-scale differences in sediment on meiofauna.