The Manado area (Indonesia–North Sulawesi), a marine high diversity hot-spot, hosts 7 species of anemonefish (family Pomacentridae, subfamily Amphiprioniae) living in symbiosis with 9 species of sea anemones (family Stichodactylidae and Actiniidae). This high biological diversity −27% and 80%, respectively, of the total known diversity of anemonefish and sea anemones—allows us to test different hypotheses focused on the obligate mutualism between anemonefish and sea anemones. In the Manado area, species richness of anemones and anemonefish across several sites was not correlated, but all anemones contained at least one fish individual, and there was a strong positive correlation between the numbers of individual anemonefish and anemones. As expected, each fish species had a preferred anemone host; also a partial niche overlap (Pianka’s Index) was often detected. The analysis of unique species composition suggests that competition is not an important factor determining the presence or absence of particular combinations of either anemonefish or host anemones (no evidence of competitive exclusion). The NODF algorithm showed that, at both a regional and local scale, the interaction between anemonefish and host anemones is not significantly nested, as a result of a combination of local conditions with competition, forcing species that regionally are more generalist to become more specialist