In recent years more attention is being paid to the presence of various non-pathogenic root fungal associations in plants of natural ecosystems for their role in various ecosystem processes. Despite their widespread reports in various ecosystems worldwide, our knowledge on root endophyte fungal association in plants from natural vegetation is far from complete. We assessed the arbuscular mycorrhizal (AM) and dark septate endophyte (DSE) fungal association in plants of Velliangiri Hills of the southern Western Ghats region, due to limited information on the root fungal association in this region. Of the 147 plant taxa (belonging to 46 families) investigated from five different vegetation types ranging from montane grasslands to tropical rainforest, 141 were colonised by AM fungi and co-occurrence of DSE fungi along with AM fungi was observed in 74 plant taxa. We report AM and DSE fungal associations for the first time in 61 and 42 plant species, respectively. Determination of AM morphological types indicated the frequent occurrence of intermediate type and AM morphology is reported for the first time in 64 plant taxa. Spore morphotypes belonging to eleven species (in six genera) were isolated from the different vegetation types. Arbuscular mycorrhizal fungal spore numbers neither differed significantly among vegetation types nor were related to AM fungal colonisation. Spores of Funneliformis geosporum was the most frequent spore morphotypes. Dark septate endophyte fungal association occurred in plants of all the vegetation types and was most frequent in herbs. Though no significant relationship was found between AM and DSE fungal colonisation within roots, a positive association was found in the occurrence of these two fungal groups.