Seabuckthorn (Hippophae salicifolia) is an economically important dioecious and deciduous actinorhizal tree species. Considering the contemporary interest in seabuckthorn as a future multipurpose crop, efforts have been initiated towards an assessment of genetic diversity prevailing in the natural populations inhabiting diverse geographical areas. In the present study, morphological and molecular diversity was studied in Hippophae salicifolia representing diverse ecological sites in the different geographical areas of the Garhwal and Kumaon regions of Uttarakhand, India. Morphological diversity was assessed by studying a total of twenty-seven morphological characters. For standard identification of the color of leaves and berries, a color-coded reference (RHS)-based study was also performed. By employing fifteen microsatellite markers, we observed 109 alleles, with 71.5% markers being polymorphic. Furthermore, Polymorphic Information Content (0.387), expected heterozygosity (He)/ Nei’s Diversity (0.641), Wright’s fixation index (Fis) (0.630), and Shannon’s informative index (I) (0.646) among the four populations were calculated simultaneously to study the phylogenetic relationship. The UPGMA-based dendrograms were also prepared by using morphological and molecular data. The dendrograms showed a demarcation between collections from different regions, although a few collections were found clustered with collections from the other regions. Assessment of genetic diversity was efficient and more informative using microsatellite markers. The findings of this study will be useful in future breeding and conservation programs in Hippophae salicifolia and related species.