Accumulating data on the increasing degradation of coral reefs worldwide has led to a focus on the unique mesophotic coral ecosystem (MCE) as a potential refuge for threatened shallow-water species (i.e., the deep reef refugia hypothesis: DRRH). Sponges play a crucial role in coral-reef functioning but are often overlooked in benthic surveys. This knowledge gap is especially true for the Red Sea, where data on sponge abundance, coverage and species composition are scarce. Furthermore, to date, no study has examined mesophotic sponges in the Red Sea. Here we compared sponge abundance and diversity metrics between shallow and mesophotic reefs at two sites in the Gulf of Aqaba, northern Red Sea. We also examined the role of biotic and abiotic parameters in determining sponge variability between sites and depths. Sponge diversity metrics significantly varied with increasing depth and between sites. Sponge species composition also differed significantly between depth and sites. However, parameters measured in the water column, that is, Total Organic Carbon (TOC), Particulate Organic Carbon (POC), NOx, etc., did not differ between depths and sites, except for Synechococcus and Prochlorococcus concentration, which did. The findings indicated that site characteristics and biotic interactions may play an essential role in determining sponge diversity and community composition. Between-site differences in sponge fauna revealed in the study highlight the importance of considering the variability in the benthic communities and the factors controlling it when designing management tools for coral reefs, particularly for the northern Red Sea.