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Enterococci are the common opportunistic pathogens having a worldwide food safety concern. The present study was undertaken to characterize the vancomycin resistant Enterococcus species of animal, human and environmental origin by using ERIC-PCR and REP-PCR assays. Out of 608 Enterococcus spp. isolates recovered by phenotypic and genotypic methods, 125 Enterococcus isolates were identified as Vancomycin resistance Enterococcus genotypically. The vancomycin resistant genes vanB, vanC1 and vanC2 were detected in 14 (11.20%), 69 (55.20%) and 42 (36.60%) Enterococcus isolates, respectively. A greater degree of heterogeneity was observed among 124 VRE isolates (one E. gallinarum isolate did not yield any bands for both ERIC-PCR and REP-PCR) of four species of Enterococcus from different sources as revealed by presence of 122 genotypes and 123 genotypes by ERIC and REP-PCR analysis, respectively. Nineteen different E. faecalis, 15 E. faecium, 57 E. gallinarum and 31 E. casseliflavus subtypes were differentiated by ERIC-PCR, whereas 21 different E. faecalis, 15 E. faecium, 56 E. gallinarum and 31 E. casseliflavus subtypes by REP-PCR. Genotypingof VRE species by ERIC-PCR and REP-PCR were found to be highly significant since discriminatory power > 0.9 are considered highly significant (0.9997 for ERIC-PCR and 0.9999 for REP-PCR). Cluster analysis also revealed a great degree of homogeneity among some VRE isolates recovered from different sources and implied at the chance of cross-contamination of foods of animal origin..