Sunflower (Helianthus annuus L.) being a cross-pollinated crop, genetic adulteration is a vested problem and varietal description is cumbersome. An investigation was carried out using sunflower hybrids, their parental lines and open pollinated varieties to identify and establish phylogenetic relationships among genotypes and characterize them based on both morphometric traits and PCR based RAPD markers. Data on twelve quantitative traits and thirty two quantitative traits were analyzed. Data for 5 primers were used to establish genetic distance and construct dendrograms using statistical software package. Based on the analysis of clustering of sunflower genotypes it was found that morphometric traits were not in accordance with the molecular markers. At the molecular level, 25 scorable bands were produced with the 5 primers with the number of bands ranging from 3 for OPH-15 to 9 for OPG-10. Of the 25 bands, 14 were polymorphic (58.11%). A male specific third fragment amplified by the primer OPI-16 was inherited by the hybrid KBSH-1 and the primer OPH-15 failed to amplify DNA from all the varieties except Morden.