Epibiotic associations can result in co-introductions of non-indigenous species, which may affect ecosystems in several ways. In fouling communities of three estuaries in southern Brazil, a number of amphipods was found to harbour a dense coverage of epibionts. Three different species, the two globally widespread caprellids Caprella equilibra and Paracaprella pusilla, as well as the ischyrocerid Jassa valida, had been colonised by diatoms. Further scanning electron microscope analyses assigned these diatoms to 14 different species that had previously been reported from benthic habitats. This is one of the scarce records of diatoms attached to amphipods. The occurrence of the diatom Amphora helenensis represents the first report for Brazilian waters as well as the second record for the whole SW Atlantic Ocean. As some diatoms were associated with common fouling amphipods, a possible regional spread aided by these crustaceans seems likely. Possible effects of this amphipod-diatom association on the animals and their implications for the underlying ecosystems of this remain to be elucidated.