The Antarctic continent harbors unique ecosystems, including diverse microbial communities inhabiting rocky substrates. Despite extensive research on Antarctic microbial ecology, a gap in knowledge persists regarding the comparative analysis of microbial communities associated with Antarctic granite rocks and the microenvironment created by the thalli of the epilithic lichens growing on them. The present study addresses this gap. Using high-throughput sequencing approaches we conducted a comprehensive comparative analysis of fungal and bacterial communities colonizing endolithic and epilithic niches on granites in Antarctica. Our results revealed distinct differences between endolithic and epilithic communities in terms of diversity and composition. Lecanoromycetes was the most frequent fungal class in both groups, which accounts for 78.5% in the endolithic and 53.5% in the epilithic samples, respectively. The prevalence of lichenized fungi in both habitats suggests their pivotal role in shaping the diversity and composition of the Antarctic microbial communities. Endolithic communities exhibited higher bacterial diversity, most probably influenced by a combination of environmental factors and the complex interplay between lichens and other microorganisms. Stress-resistant bacterial taxa, as the radioresistant Truepera and Rubrobacter species were specifically found in the endolithically colonized specimens, suggesting that the endolithic lifestyle promotes a more specific ability to adapt throughout environmental extremes. Moreover, the endolithic niche in granites seems to positively select cyanobacteria, as they were found to play a significant role in endolithic communities, demonstrating their adaptability to low-light conditions and their importance in nutrient cycling. Overall, our findings shed light on the ecological dynamics of microbial communities in extreme environments and highlight the importance of further research to elucidate their roles in Antarctic ecosystems. Keywords: Antarctica · Epilithic lichens · Metabarcoding · Endolithic microbial communities · Granites.