Antarctica is one of the most stressful ecosystems worldwide with few vascular plants, which are limited by abiotic conditions. Here, plants such as Deschampsia antarctica (Da) could generate more suitable micro-environmental conditions for the establishment of other plants as Colobanthus quitensis (Cq). Although, plant-plant interaction is known to determine the plant performance, little is known about how microorganisms might modulate the ability of plants to cope with stressful environmental conditions. Several reports have focused on the possible ecological roles of microorganism with vascular plants, but if the rizospheric microorganisms can modulate the positive interactions among vascular Antarctic plants has been seldom assessed. In this study, we compared the rhizosphere microbiomes associated with Cq, either growing alone or associated with Da, using a shotgun metagenomic DNA sequencing approach and using eggNOG for comparative and functional metagenomics. Overall, results show higher diversity of taxonomic and functional groups in rhizospheric soil from Cq+Da than Cq. On the other hand, functional annotation shows that microorganisms from rhizospheric soil from Cq+Da have a significantly higher representation of genes associated to metabolic functions related with environmental stress tolerance than Cq soils. Additional research is needed to explore both the biological impact of these higher activities in terms of gene transfer on plant performance and in turn help to explain the still unsolved enigma about the strategy deployed by Cq to inhabit and cope with harsh conditions prevailing in Antarctica.