Molecular characterization of 19 advanced cultivars and landraces of brinjal was carried out using RAPD and ISSR markers. Twenty-nine RAPD primers generated a total of 240 amplified fragments, while 23 anchored and non-anchored ISSR primers produced 299 fragments. Of these, 66 (27.5%) RAPD and 56 (18.73%) ISSR fragments were polymorphic. All the cultivars could be distinguished based on RAPD and/or ISSR profiles. A set of two RAPD primers, OPW 11 and OPX 07, was adequate to distinguish all the 19 cultivars. On the other hand, a minimum of ten ISSR primers were required to achieve the same result. Eleven cultivars could be identified by the unique presence or absence of one to four markers. The correlation between primer Rp and the number of cultivars distinguished by RAPD was r = 0.873, while that for ISSR it was r = 0.327. The correlation between PIC of primer and the number of cultivars distinguished was r = 0.324 for RAPD, while for ISSR primers it was r = − 0.066. The probability of chance identity between two cultivars for RAPD and ISSR markers was calculated as 8.94×10−4 and 2.25×10−2, respectively. The average Jaccard’s similarity coefficient between cultivars based on combined RAPD and ISSR data was estimated to be 0.919. The UPGMA analysis grouped the cultivars into three main clusters with significant bootstrap support. While the cultivars bred at Indian Agricultural Research Institute, New Delhi formed one sub-cluster; others did not show a prominent region-based clustering.
