The domesticated apple (Malus x domestica Borkh) is one of the most widely cultivated fruit crop of the temperate world. Large number of commercial cultivars and varieties are available which need an accurate characterization to be used in the breeding programmes. Keeping this thing in mind, the genetic diversity among 46 genotypes was investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 130 amplification products were detected with 21 ISSR primers of which 130 (100%) were reported to be polymorphic. Primers based on (AC)n and (AG)n repeats produced more polymorphic bands. The number of bands generated by 21 ISSR primers ranged from 4(UBC 840) to 10 (ISSR 3) with a mean of 6.19 bands per primer. The band size ranged from 300-1700bp. The Jaccard's similarity coefficient ranged from 0.435 to 0.822 suggesting that the 46 genotypes used in the study were highly divergent. Cluster analysis based on the UPGMA method and bootstrap analysis separated all the genotypes into three major clusters. Maximum Resolving Power (Rp) was computed to be 5.696 (ISSR 3) while the minimum was 1.174 (UBC 850). The highest Polymorphism Information Content (PIC) was recorded to be 3.946 (ISSR 3) while the lowest was 1.700 (UBC 850). The overall Heterozygosity Averages (H av) values of primers were 0.068 and 0.717 respectively for ISSR and UBC series. The present study has successfully distinguished morphologically similar genotypes that emphasize the use of molecular markers to the taxonomists.