The study of biological invasions can be roughly divided into three parts: detection, monitoring, mitigation. Here, our objectives were to describe the marine fauna of the area of the port of São Sebastião (on the northern coast of the state of São Paulo, in the São Sebastião Channel, SSC) to detect introduced species. Descriptions of the faunal community of the SSC with respect to native and allochthonous (invasive or potentially so) diversity are lacking for all invertebrate groups. Sampling was carried out by specialists within each taxonomic group, in December 2009, following the protocol of the Rapid Assessment Survey (RAS) in three areas with artificial structures as substrates. A total of 142 species were identified (61 native, 15 introduced, 62 cryptogenic, 4 not classified), of which 17 were Polychaeta (12, 1, 1, 3), 24 Ascidiacea (3, 6, 15, 0), 36 Bryozoa (17, 0, 18, 1), 27 Cmdana (2, 1, 24, 0), 20 Crustacea (11, 4, 5, 0), 2 Entoprocta (native), 16 Mollusca (13, 3, 0, 0). Twelve species are new occurrences for the SSC. Among the introduced taxa, two are new for coastal Brazil. Estimates of introduced taxa are conservative as the results of molecular studies suggest that some species previously considered cryptogenic are indeed introduced. We emphasize that the large number of cryptogenic species illustrates the need for a long-term monitoring program, especially in areas most susceptible to bioinvasion. We conclude that rapid assessment studies, even in relatively well-known regions, can be very useful for the detection of introduced species and we recommend that they be carried out on a larger scale in all ports with heavy ship traffic.