Hindu Kush is the largest mountain range of Central Asia that forms part of a vast alpine zone that stretches across the Eurasia from east towards the South Asia. We studied vegetation structure and the role of edaphic and topographic factors on distribution and formation of plant associations with specific emphais on Parrotiopsis species of the Districts Dir regions in the Hindu Kush Mountains. We also assessed the conservation status of Parrotiopsis jacquemontiana, an endemic species of the western Himalayan floristic province. We hypothesized that edaphic and climatic factors were responsible for the formation of different plant associations each with distinct indicators. A combination of transect and quadrat based methods were used for sampling. We used two way cluster analysis (TWCA), cluster analysis (CA), indicator species analysis, detrended correspondence analysis and canonical correspondence analysis to analyze and elaborate the vegetation pattern and formation. We used Google Earth Path software (V 1.4.6) for the calculation of extant of occurrence (EOO) and area of occupancy (AOO) for evaluation of conservation status of P. jacquemontiana. A total of 142 plant species were reported belonging to 62 families. CA and TWCA clustered four plant associations within altitudinal range of 1556–2313 m. Parrotiopsis jacquemontiana should be designated as endangered species under ‘EN A2acd; B1B2 bc (i, ii, iii) of IUCN red list categories and criteria in the region. We found that high phosphorous and potassium concentration, elevation, aspect, slope, lower pH, electrical conductivity and soil texture were significant environmental variables that play an important role in the determination of vegetation structure, formation of plant associations and its indicators in the region. This information will be useful for conservation and management practices for endemic and rare plant taxa, and evaluation of vegetation structure.