The city of São Sebastião (SS), in south-eastern Brazil, is one of the hotspots for marine research since the establishment of the Centre of Marine Biology of the University of São Paulo in the 1960s. The SS region experienced intense transformation during the past 50 years, including increasing urbanization and construction of maritime facilities. Ascidian surveys during the past 50 years have found 62 species, eight of which were described as new and 12 are introduced. Didemnidae and Styelidae are the most speciose families in São Sebastião Channel, with 20 and 15 species respectively. Phallusia nigra, Didemnum psammatodes, Trididemnum orbiculatum, Botrylloides nigrum and Symplegma rubra are the most common ascidians. Most of the species are of tropical origin and São Paulo is their southern geographical limit. Comparisons of reports of the ascidians from different time periods allowed detection of species introductions and shifts in assemblage structure in terms of both species composition and abundance. Additionally, we discuss the main taxonomic issues regarding ascidians from south-eastern Brazil and identify profitable areas for future research. We believe that the temporal data compiled here will serve as a baseline for monitoring and management of ascidians in SS. Additionally, this study provides one of the most detailed datasets of ascidian diversity from the south-western Atlantic Ocean.