The current study is a pioneering effort to create karyotypes and include comprehensive karyomorphological analysis of two wild species (M. sar-gharwalensis from Uttarakhand containing high protein content of 39.5% and M. axillare from Australia with significant characters, such as more pods/plant, a larger seed yield/plant, stress tolerance etc.) and one cultivated species (M. uniflorum) of horsegram. For genetic diversity study eight cultivated lines (VLG1, HPKM319, HPKM317, HPKM249, HPKM193, HPK4, HPKM191, HIMGANGA) along with wild species were analyzed with 50 SSRs primers. Cytogenetic markers like secondary constrictions, 45S rDNA and 5S rDNA were established in this study. Over 200 crossing attempts between cultivated and wild species resulted only six F1, which were sterile. The cause of the F1's sterility was identified by studying pollen morphology, meiotic anomalies, and chromosomal data. The phylogenetic tree was drawn from the molecular analysis using DARwin software. All results were in consonance with the other results yielded by Dendogram and Structure analysis. Dendrogram showed that M. sar-gharwalensis is completely distinct from the cultivated lines, whereas M. axillare found to be very close to them. HIMGANGA and HPKM193 lines of cultivated species exhibited more resemblance towards M. axillare as compared to the other species. Molecular characterization and karyotypic studies marked M. axillare as the closest parent of the cultivated horsegram (M. uniflorum). These findings would be extremely beneficial in clarifying the phylogenetic relationships and extending the limited genetic base of the cultivated species of horsegram for further enhancing its nutritional and therapeutic properties.