Collection and characterization of local genotypes and landraces are prerequisite for any crop improvement program. Molecular diversity and DNA profiling shown exact genetic blue print of any crop. Hence, the experiment was design to establish the molecular diversity and polymorphism among some local eggplant genotypes and its wild relatives for future breeding program. The experiment was carried out at the Biotechnology Laboratory, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh, with twenty-five local and two wild relatives (Solanum sisymbriifolium and S. villosum) of eggplant to study molecular diversity and DNA fingerprinting at those genotypes. Five well-known SSR primers (EPSSR82, smSSR01, EM114, EM120 and smSSR04) were used for the molecular characterization of the genotypes. Quality DNA was isolated with 27 genotypes and PCR amplification was carried out with these primer. The amplified DNA fragment was visualized by 2% agarose gel and data were analyzed by POWERMAKER (version 3.25) and NTSYS-PC (version 2.2). Some total at 10 different alleles were generated with a range of 1 to 3 alleles per locus and an average of 2.0 alleles. The highest number (2) of polymorphic bands was observed in the primers EPSSR82 and smSSR01. The Polymorphism Information Content (PIC) of SSR markers ranged from 0.37 to 0.67 with an average value of PIC = 0.54. Gene diversity ranges from 0.49 (smSSR01) to 0.72 (EPSSR82), with an average value of 0.61. UPGMA method separated the of 27 genotypes into two major clusters (I and II). From the clusters, wild species Solanum villosum belonged to the sub-cluster (IIb), that revealed its distinct variation from the others. On the other hand, wild species Solanum sisymbriifolium showed a close relatedness by forming the same cluster together with thirteen local eggplant genotypes. Molecular diversity and DNA profiling was identified among 25 local eggplant germplasm and its wild relatives. The finding of the experiment could be used for selection of diverse parent for eggplant improvement.