The fauna associated to the sponge Sarcotragus foetidus was studied in two eco-regions of the Mediterranean Sea, the Aegean and Levantine Seas. A total of 134 species belonging to 8 taxonomic groups were determined. Different species assemblages were encountered in the eco-regions, mainly due to the importance of some alien species (Red Sea invaders) on sponge communities. Among community parameters, only the number of species differed significantly among the sub-regions. The number of species and the number of individuals were significantly and positively correlated with the sponge volume. The species assemblage patterns determined were significant correlated with a set of environmental variables such as nitrogen, phosphate and dissolved oxygen. Some alien species such as the ophiuroid Ophiactis savignyi and the polychaete Leonnates indicus densely invaded porous systems of sponges in the Levantine Sea, indicating the magnitude of impacts of alien species on the eastern Mediterranean ecosystem. In the Levantine Sea, the alien species accounted for 34% of total number of individuals of macro-invertebrates associated with sponges, but the percentage rose up to 64% in Iskenderun Bay (eastern-most point of studied area). The biotic index ALEX detected a moderate ecological status in the area in terms of the impacts of alien species on native biodiversity.