Meiofauna from three seagrass beds in the southern Egyptian Red Sea coast was quantitatively studied. Sediment samples were collected in May 2021 at a depth of 1.5-2 m meters from the sand underneath the seagrass and their adjacent unvegetated sediments at two sites. In the two habitats under study, Marsa Assalya and Marsa Mobarak, the former showed the highest abundance of meiofauna, whereas the latter attained the lowest densities. Meiofaunal communities in the seagrass beds were more diversified than in the adjacent unvegetated sediments which contrarily showed more individual counts. 14 major taxa were recorded; Nematoda was the most common taxa in seagrass beds, while Copepoda was the abundant group in the unvegetated sediments. Significant correlations were found between sediment characteristics and some major meiofaunal taxa. A total of 21 nematode genera were determined. Epistrate feeding was the dominant type and Daptonema was the most abundant genus in both habitats. The different structures of meiofaunal communities distinguish each habitat within the same sites rather than their geographical distribution.