The Antarctic ecosystem is one of the most stressful natural habitats, especially for terrestrial plants. Likewise, only two vascular plants have colonized the Antarctic environment, Colobanthus quitensis (Caryophyllaceae) and Deschampsia antaractica (Poaceae). Although both plants colonize Antarctica, C. quitensis is mainly found growing in association with D. antarctica in more stressful areas, while D. antarctica is capable to grow alone in areas with higher abiotic stress. Positive inter-specific interactions play a pivotal role in the structure and functioning of several ecosystems in harsh environments, and possibly they play a role in Antarctic terrestrial ecosystems.</p><p>In this study, we compare the rhizosphere microbiomes associated with Colobanthus quitensis, either growing alone or associated with Deschampsia antarctica, using shotgun metagenomic DNA sequencing technology for comparative metagenomics. This approach allows us to gain insight into the rhizospheric microbial community structure associated with C. quitensis and C. quitensis – D. antarctica, through the study of soil’s microbial taxonomic diversity, including non-culturable organisms. Such analysis could also provide valuable information regarding microbial functional diversity. This functional diversity might be playing important roles in conferring different degrees of tolerance to Antarctica’s harsh environmental conditions such as low temperatures, desiccation, and low water and nutrient availability, which could help to explain the “enigma” of the success of these plant species in such harsh environments.