In the present palyno-morphometric studies in the genus Indigofera from Karnataka were analyzed with the support like principal component analysis, principal co-ordinate analysis, cluster analysis and light microscopy technique. Pollen dimensions were measured by considering quantitative characters viz. equatorial diameter, polar diameter, P/E ratio and numbers of apertures. It was observed that the mean polar dimension ranges from 2.13 μm to 3.35 μm while equatorial dimension ranges from 1.68 μm to 3.65 μm. Based on the obtained results correlation matrix reveals positive significant relationship between polar diameter and equatorial diameter in contrast with this distance matrix shows great similarities between Indigofera cordifolia-Indigofera linifolia, Indigofera hirsuta- Indigofera linifolia, Indigofera hochstetteri-Indigofera karnatakana- Indigofera uniflora, Indigofera karnatakana-Indigofera uniflora, Indigofera tinctoria-Indigofera trita. Among all species Indigofera caerulea -Indigofera glandulosa shows greater variation, whereas Indigofera karnatakana-Indigofera uniflora shows closely positive significant relationship. In conclusion the study was demonstrated the usage of such analysis in taxonomic research will solve the doubtful grouping of the species.