Background: Comparing meiofaunal assemblages in the seagrass zone with bare sediment will provide information on the structuring factors and phytal preferences of meiobenthic invertebrates since differences in density and diversity of meiofauna are to be expected between vegetated and bare zones. Results: A total of 11 groups of meiofauna, with harpacticoids dominating (51 %) and comprising 48 species within 14 families, have been identified. At all localities, the following harpacticoids were found to be relatively abundant, contributing 30.9 % of all harpacticoids: Longipedia weberi, Canuellina nicobaris, Scottolana longipes, and Parastenhelia hornelli. A highly significant correlation (r = 0.987, r 2 = 0.974, F (1,9) = 337.3, P < 0.001) of meiofaunal assemblage was found between seagrass leaf blades and the canopy sediment compared to bare sediment which was found to have a moderate correlation (r = 0.543, r 2 = 0.294, F (1,9) = 3.756, P = 0.085). In addition, the abundance of harpacticoids was significantly higher (ANOVA, F (2,144) = 19.53, P < 0.001) in seagrass sediments and differed markedly from blades and bare sediments, and the composition was unique in the different zones of the present study. Conclusions: Productive seagrass ecosystems are as yet inadequately studied in the Andaman Islands. This study provides a first step to characterize a faunal group from the seagrass community.