The marine waters around the South Shetland Islands are paramount in the primary production of this Antarctic ecosystem. With the increasing effects of climate change and the annual retreat of the ice shelf, the importance of macroalgae and their diatom epiphytes in primary production also increases. The relationships and interactions between these organisms have scarcely been studied in Antarctica, and even less in the volcanic ecosystem of Deception Island, which can be seen as a natural proxy of climate change in Antarctica because of its vulcanism, and the open marine system of Livingston Island. In this study we investigated the composition of the diatom communities in the context of their macroalgal hosts and different environmental factors. We used a non-acidic method for diatom digestion, followed by slidescanning and diatom identification by manual annotation through a web-browser-based image annotation platform. Epiphytic diatom species richness was higher on Deception Island as a whole, whereas individual macroalgal specimens harboured richer diatom assemblages on Livingston Island. We hypothesize this a possible result of a higher diversity of ecological niches in the unique volcanic environment of Deception Island. Overall, our study revealed higher species richness and diversity than previous studies of macroalgae-inhabiting diatoms in Antarctica, which could however be the result of the different preparation methodologies used in the different studies, rather than an indication of a higher species richness on Deception Island and Livingston Island than other Antarctic localities.