Submerged Aquatic Vegetation (SAV) in coastal habitats plays critical roles because it protects coastlines, prevents erosion, provides nursery habitat, and dissolved oxygen. Meiobenthic communities in these habitats also play a key role in ecosystems processes. However, currently SAV loss continues unabated globally. Our understanding of the impact this loss has on meiobenthic communities is limited. To assess the impact of SAV cover on nematode communities, we studied nematode communities at Currituck Sound, NC, by comparing communities at an unvegetated and at an SAV site. Nematodes were identified to genus level morphologically. Our results showed that general diversity was low compared to other comparable sites with only 10 genera at both sites. Diversity and community structure were distinct at the two sites indicating that submerged aquatic vegetation may impact community structure of nematodes.