The species composition of the epiphytic benthic foraminiferal fauna was compared at two coastal locations in the Aegean Sea. Samples were collected during August 2001 and July 2003 along the southeastern coast of Andros Island at Korthi Gulf, where there are minimal anthropogenic activities, and at Kastro Gulf, with substantial anthropogenic influence. This study represents the first application of the FORAM Index (FI), which is a single-metric index for water quality originally developed for western Atlantic reef foraminiferal assemblages, to Mediterranean assemblages. Multivariate analyses distinguished three clusters of sample sites representing three foraminiferal assemblages. Samples dominated by the mixotrophic species, A. lobifera, were collected primarily from sites along the northern coasts of both gulfs. Characteristics of this assemblage, including relatively high dominance (D=0.27–0.51), lower Shannon–Wiener diversity (H′=1.3–2.1) and high FI (6.6–8.2), all reflect oligotrophic environmental conditions typical of pristine waters of the Aegean Sea. A. lobifera was typically the most common species in the second assemblage, though relative abundances of heterotrophic taxa were higher, resulting in somewhat higher diversity (H′=1.6–2.4) and lower dominance (D=0.14–0.36). These indices, as well as the FI range of 3.5–7.0 indicated somewhat more prevalent organic carbon resources but still relatively high water quality. This assemblage was found along the southern coast of Korthi Gulf and at more interior sites in northern Kastro Gulf. The third assemblage was dominated by smaller heterotrophic species, including notable proportions of the stress-tolerant taxa Ammonia spp. and Elphidium spp., and had few or no A. lobifera. Diversity (H′=1.4–2.0) and dominance (D=0.22–0.47) indices were similar to those for the first assemblage, but FI values were much lower (2.0–3.4). Samples characterized by this assemblage were collected only from the southern Kastro Gulf, in the vicinity of the primary sewage outfall. The results of this study document the sensitivity of benthic foraminiferal assemblages, and particularly A. lobifera populations, to sewage pollution in the Aegean Sea. These observations are consistent with studies from other biogeographic regions where the FORAM Index, which is based upon this genus and associated mixotrophic taxa, has been used as a water-quality indicator. This observation is particularly noteworthy because A. lobifera is an invasive species in the Mediterranean.