Here we describe new microfossil assemblages for the Miocene Hobbs Glacier Formation and the first possibly indigenous assemblages for the Plio-Pleistocene Weddell Sea Formation on Seymour Island, West Antarctica. The assemblages are composed mainly of foraminifers, but radiolarians, calcitarchs and poriferan sclerites are also present. For the Hobbs Glacier Formation, we report the foraminifers Bolivina sp., Oolina globosa and Rosalina cf. globularis; and for the Weddell Sea Formation, we report Favulina hexagona, Globigerinita uvula, Globocassidulina cf. subglobosa and Psammosphaera fusca. The low abundance and diversity of microfossils, allied with the complex taphonomical processes that prevailed in Antarctic glacial–marine palaeoenvironments, make it impossible to define whether the assemblages are composed of a mixture of indigenous and re-elaborated specimens or exclusively of re-elaborated remains. Nevertheless, the indigenous nature of some specimens is suggested by their inherent fragility, excellent preservation and/or taxonomic association with indigenous assemblages from correlated strata. The taxonomic compositions are not directly comparable with other Antarctic assemblages, although most of the species were previously reported from pre-Quaternary or modern deposits of both West and East Antarctica. This lack of correspondence is probably due to preservation biases, but any further significance is hidden by the complex taphonomy of the deposits.