The Island of Santa Catarina is a mosaic of ecosystems of great importance for fish fauna, highlighting the presence, in the same island, of estuaries, lagoons, mangroves, rocky shores and sandy beaches. This study aimed to compare, based on species richness, fish assemblages between different ecosystems. Between 1981 and 2011, there were collected a total of 165 taxa of fish, distributed in 54 families, in six sampling sites, using casting net, sweep net, beach trawl and gill net. According to the species accumulation curve, that show the increase of the number of different species with the increase of the number of samples, for all sites, the curves of species recorded followed patterns similar to curves obtained by the Jacknife index. However, the number of species has stabilized only for samples collected in Saco dos Limões, Itacorubi Mangrove and Ratones Mangrove. Comparing the mean values of richness between sites, the highest mean value was found in Saco dos Limões, followed by Índio Beach, Conceição Lagoon, North Bay , Itacorubi and Ratones Mangroves. Using the list of species as reference, despite the differences in abundance and richness between sites, the taxonomic structure is similar between sampling sites, which supports the hypothesis that the assemblages are occurring in all sites and the differences are primarily related to the patterns of reproduction and recruitment of species and secondarily influenced by abiotic factors, especially the temperature and salinity.