Seagrass beds are highly diverse and productive marine habitats for many associated organisms in nearshore coastal waters. The differences in abundance, diversity, and community structure of benthic invertebrates between seagrass beds and adjacent unvegetated sediments have been stated, whereas most studies are primarily focused on macrofauna or based on a comparatively long distance, i.e., more than 10 m. The present study is designed to test if the community structures of meiofauna, especially the free-living nematodes, differ between seagrass beds and adjacent unvegetated sediments on a meter scale. There are 21 meiofaunal taxa and 63 nematode genera that have been identified from a tropical seagrass bedof Thalassia hemprichii inLudao, Taiwan. Although the compositions of higher meiofaunal taxa are undistinguished, according to correspondence analysis, the assemblages of nematode genera differ substantially between the seagrass bed and unvegetated sediments. Regarding the nematodes, approximately 50% of genera are restricted to the seagrass bed whereas 6% are restricted to unvegetated sediments, which indicate both habitats possessing distinct infaunas. The number of replicates for reasonable estimation of the local diversity index is calculated by the randomization technique. For local seagrass beds, only a single core is sufficient for reliably estimating meiofaunal diversity, but at least three cores or a sample size of 300 individuals is needed for the nematode community. Nematode assemblages provide more particular differences between seagrass and unvegetated habitats than meiofaunal communities on small spatial scales. Both seagrass beds and adjacent unvegetated sediments harbor specific meiofaunal communities, and hence, the conservation strategy for seagrass should also consider the peripheral bare area of seagrass beds.