The evaluation of fungal root endophytes of two multizonal mountain plant species (Soldanella carpatica and Homogyne alpine) in relation to altitude was conducted. The comparison of root colonization by coarse arbuscular mycorrhizal fungi (AMF) and the fine AMF endophyte (Glomus tenue), as well as the presence of dark septate endophytes (DSE) were assessed along altitudinal gradients (1000–2050 m a.s.l.) on calcareous and non-calcareous substrata in the Tatra Mts. (Western Carpathians). Additionally, AMF species composition in the rhizosphere of the investigated plants was determined. Coarse AMF dominated over the fine endophyte in roots of S. carpatica and H. alpina. In the case of S. carpatica, there was a tendency for coarse AMF colonization decline with increasing altitude, while the reverse trend was observed for the fine endophyte. In contrast, the altitudinal patterns of the two types were opposite in H. alpina. Fifteen AMF species associated with the rhizosphere of S. carpatica were identified at the sites located in the Western Tatra Mountains, whereas spores of only four species were isolated from the rhizosphere of H. alpina in the High Tatra Mountains. None of the identified AMF species was observed to occur both in the High and Western Tatra Mts. DSE accompanied AMF in the roots of S. carpatica and H. alpina at each site; however, the root colonization by this group of fungi was low. The DSE colonization did not have a consistent relationship with altitude in both plant species. The results suggest that at the investigated altitudes factors such as the type of substrata, host plants, and local plant species composition may play a more important role in determining root colonization as well as the establishment of a local AMF community than the climatic changes with increasing elevation above sea level.