Comprehensive studies on meiotic behavior and pollen biology of a species are crucial for its conservation strategies. The presence of meiotic bottlenecks directly or indirectly influences the reproductive success of a plant species. The present study records chromosome number, male meiotic behavior, seed set, pollen viability, and pollen germination in two populations of Swertia thomsonii, an important medicinal plant of Himalaya. The chromosome count recorded in both accessions was 2n=2x=26, however; chromosomal abnormalities (21.23 and 4.31%) were recorded in population 1 (Pop-1) and population 2 (Pop-2), respectively. These include chromosomal stickiness, out of the plate, formation of laggards, abnormal spindles, bridges, multipolarity, and polysporads. These meiotic irregularities compromise pollen viability, pollen germination, and seed set of species. The possible cause for these recorded meiotic abnormalities was cold stress as the species grows in temperate or sub-alpine regions with cold climatic conditions. Another possible reason might be the presence of heavy metals in the soil more than permissible limits, which was determined by soil sample analysis. Therefore, these findings along with other reproductive and ecological studies can aid in the development of successful conservation and management strategies for this medicinally important plant species.