Here, we aimed to evaluate the influence of the plant-host identity and habitat conditions on structuring the plant fungal endophytic community but moreover, to estimate their local adaptive role assessing their effect on the fitness of both native plant hosts. For this, we combined a descriptive metagenomic analysis with a reciprocal transplant experiment using plants with and without its fungal endophytes to: i) characterize the variation in fungal communities among plant species (Colobanthus quitensis and Deschampsia antarctica), plant tissues (roots and leaves), and habitats (hill and coast) of the Maritime Antarctica, and ii) to determine the role of those endophytic microorganisms in plant capacity to cope with the different ecological settings in Antarctica. Overall, from the 108 fungal taxa found among both plant hosts, 68 for C. quitensis and 81 for D. antarctica, a 5 and 13% of unique genera were found for the former in hill and coast habitats, respectively, while for D. antarctica this proportion represented a 13 and 16%. The Bray-Curtis and the ordination analyses showed, however, a significant role of both, plant species and local habitat, in structuring the host fungal endophytic community, being the later particularly evident in D. antarctica. Finally, a higher average mortality and the reduced mean final biomass showed by cross-transplanted plants (e.g.: from coast-to-hill), relative to auto transplanted individuals (e.g.: from hill-to-hill) in D. antarctica, suggesting a microbe-mediated process of local adaptation for this species. These results may imply that both native plants are following different ecological strategies (generalist or specialist) regarding their interaction with fungal endophytes, an aspect that might be determinant in explaining their current and future patterns of distribution among Antarctic ecosystems.