Cytology, morphology and ecology were determined from 21 natural populations of Aconitum heterophyllum in Kashmir and Ladakh Himalayas. Data revealed a high body of variability among various morphological characters including plant height, foliage, floral and tuber attributes at intra-population levels. Plant height varied from 98 ± 4.6cm to 36.1 ± 4.5cm. The tuber crude drug production values ranged from 1.22 to 1.7 g/plant. It was generally lower at lower altitudes and higher at higher altitudes. The number of flowers varied from nine to 11; however, it was directly linked with altitude. A similar trend was observed for number of seeds/fruit. Despite this variability, the species was restricted to specific ecological niches with critically low population density facing onslaught of over-exploitation. The present study contributes to insight some aspects of the cytogenetic diversity related to the distribution range of the studied populations with respect to different ecological factors. In addition, the chromosome study depicted that all the populations were diploid (2n = 16); however, the meiotic course varied from normal to abnormal with 11 populations showing abnormalities. These populations exhibited reduction of pollen fertilities up to 20-40% as well as formation of heterogeneous sized pollen grains.