Mountain ecosystems are recognized for their sensitivity to climate change, mainly due to the influence of low temperature on ecological processes. These ecosystems are likely to be dominated by the cold adapted microbial communities. Such unique ecosystems extend the opportunity to identify the bioindicators, much needed in the present scenario of climate change. In natural ecosystems, plants harbor a variety of endophytic microorganisms where the fungal endophytes, ascomycota in particular, are most abundant. The plant-fungal symbiosis is likely to be decisive in predicting the ecosystem response to global change. Among the known fungal endophytes, the dark septate endophytes (DSE) are restricted to plant roots and distinguished by the presence of dark septate hyphae and microsclerotia. The melanin content, found in these endophytes provides protection to the hyphae against biotic or abiotic or both kind of stresses and play significant role in their survival, and the adaptation of the host plant under stressed climatic conditions. DSE are being reported to colonize the root tissues of the host species from tropics to arctic and alpine habitats. Himalaya is known as one of the globally recognized hotspots of biodiversity due to its unique climate and rich biodiversity. The focus of this presentation will be on some recent reports emanated on the colonization of DSE in agricultural and forest species in high altitudes of Indian Himalayan region. Increasing knowledge on the colonization of the high altitude plants classifies these organisms as bioindicators of climate.