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 gentle non-acidic method for diatom digestion, followed by an established slide scanner protocol to increase transparency and repeatability of diatom identification. The results showed that epiphytic diatom species richness was higher on Deception Island as a whole, while individual hosts showed higher richness 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 in other studied locations in Antarctica, which could be the result of the different preparation methodologies used in the different studies and which underlines the necessity of a repeatable and transparent methodology such as the one presented in this paper. In conclusion, this study not only explores differences in distribution of epiphytic diatoms according to macroalgal host and location thereof, but also proposes a methodology which can can facilitate the identification of diatoms and the appraisal of biodiversity in naturally stressed and nearly pristine ecosystems.