Meiofauna from three coral reef sites in Marsa Alam along the Egyptian Red Sea coast was quantitatively studied. Sediment samples were collected from a depth of 7 meters from the sand flat between the seagrass bed and the reef crest in each site. Water temperature and salinity were homogeneous, while the sediment's median grain sizes and total organic matter percentages varied. Total densities were higher in sites II and III and showed relatively similar sediment characteristics than that found in site I. Nematoda (38%), Copepoda (25%), and Polychaeta (22%) were the most common taxa at all investigated sites, with a maximum in August and a minimum in February. Spearman correlation coefficients showed significantly strong positive values between all meiofaunal taxa and temperature. A total of 10 nematode families were recorded. Among them, Chromadoridae, Cyatholaimidae, and Xyalidae were the most abundant (74%). Epi-growth feeding dominated all feeding types and accounted for 73% of total nematodes. The high similarities in the meiofaunal and nematofaunal composition among sites suggested the significance of sediment characteristics as a factor impacting community structure.