Background and Aims <p>The liverwort <i>Marchantia polymorpha</i> cannot associate with arbuscular mycorrhizal fungi but hosts other endophytes that may aid to cope with environmental conditions. The impact of human disturbance on the composition and function of these fungal communities remains poorly understood. Here, we characterized the endophytic fungal community and its functional traits in natural populations of <i>M. polymorpha</i> from sites with varying degrees of human disturbance.</p> Methods <p>We combined culture isolation and metabarcoding (ITS sequencing) to characterize endophytic communities from three sampling sites. We assessed taxonomic diversity and phosphorus-related enzymatic activities to investigate potential shifts in microbial communities.</p> Results <p>Endophytic fungal community composition, as revealed by culturing, varied sites with varying human disturbance. Functional assays indicated that isolates from the more disturbed sites tended to display higher phosphatase activity and a greater capacity to solubilize inorganic phosphorus in vitro, suggesting a potential shift in functional profiles. Notably, several Mucoromycotina isolates were recovered from all sampling sites, highlighting their potential role as a natural endophyte of <i>M. polymorpha.</i></p> Conclusions <p>Our exploratory study reveals that anthropogenic disturbance affects fungal endophyte community of <i>M. polymorpha</i>. While we observed increased in vitro phosphorus solubilization traits in isolates from disturbed sites—suggesting a microbial adaptation to nutrient stress—these functional differences across sites warrant further investigation. This work points to the potential of Mucoromycotina fungi to thrive within the <i>M. polymorpha</i> thallus and highlights the need for further replicated studies to confirm these patterns and their ecological implications.</p>