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Plant biodiversity of some of the high-altitude national parks of Indian Himalaya is increasingly experiencing anthropogenic pressure. Consequently, plant species composition, vegetation structure, and diversity patterns of these protected areas are assumed to be substantially altered. However, limited efforts are made to quantify the impact of anthropogenic disturbances on the species richness of such high-altitude national parks of Indian Himalaya. To overcome this data gap, this study is aimed at quantifying the impact of anthropogenic disturbances on the vegetation community patterns of two Indian Himalayan National Parks along elevation transects, i.e., the Valley of Flowers National Park (VoFNP, altitude ranging from 3,200 to 6,700 m a.s.l.) and the Great Himalayan National Park (GHNP, altitude ranging from 1,500 to 6,000 m a.s.l.), India. The impact of anthropogenic disturbances along the elevation zone (3,200–4,500 m) on the vegetation community patterns was assessed by comparing plant species richness and diversity between selected disturbed and undisturbed sites along the altitudinal gradient. The disturbed sites, near to pathways within each national park, experienced the frequent human interventions than the undisturbed sites which were beyond 25–50 m from the pathway within each national park. Diversity profiles calculated as hill numbers (q = 0, 1, 2) showed significant variation between disturbed and undisturbed sites exhibiting high level of disturbance, especially in VoFNP. The non-metric multidimensional scaling of species composition data along the elevation of both national parks indicated that heterogeneously grouped plant species were much higher for disturbed sites than undisturbed ones. The quantum of anthropogenic pressure on disturbed sites of both VoFNP and GHNP was discernible through statistically significant lower values of soil moisture, bulk density, porosity, potassium, and phosphorous content than the undisturbed sites. As a consequence, disturbed sites were clearly noted to have lower numbers of threatened and endemic species (20 and 17, respectively) in comparison with undisturbed sites (32 and 31, respectively). The canonical correlation analyses of species compositions and soil properties of VoFNP and GHNP indicated that soil moisture and pH were the two major factors that control species composition for both disturbed and undisturbed sites, whereas soil porosity played a major role in species composition of undisturbed sites. The disturbed sites of lower elevation zones (3,200–3,500 m) of both parks were found with a higher density of invasive species (i.e., Polygonum polystachyum, Impatiens sulcata, Cuscuta europaea, etc.). Our study indicated that anthropogenic pressures on the high-altitude national parks of India not only altered the soil properties, but potentially threatened the species composition, thus accelerating urgent need to implement mitigation measures for restoration of degrading habitat of the native, endemic, and threatened plants in both the parks.