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The present investigation was carried out for the assessment of molecular diversity in parental lines of muskmelon to be used for the crossing programs to get hybrids with desirable traits. A total of eight inbred lines of andromonoecious muskmelon were assessed with twenty ISSR (Inter Simple Sequence Repeat) primers. Based on polymorphism four primers were selected for whole molecular analysis. The polymorphism varied from 50.00 to 90.90% with an average of 82.97 percent. Pair-wise similarity matrix in accordance with Jaccard’s coefficient revealed the similarity estimation ranging from 55.00% to 75.00%. The maximum similarity value was recorded for the PMM-37 (0.75) with Hara Madhu while the lowest was observed for PMM-4A (0.55) with PMM-16 and between PMM-32 (0.55) and PMM-18. Eight genotypes were categorized into two main clusters. Cluster I included 6 genotypes and Cluster II comprised 2 genotypes with approximately 70.80% similarity among themselves. Cluster I is further subdivided into two sub-clusters IA and IB with 63.00% similarity. Sub-cluster IA further forked into two small clusters IAi and IAii. IAi is comprised of PMM 4A. IAii is further subdivided into 2 groups; Group 1 and Group 2 with approximately 73.60% similarity. Group 1 consists of PMM 16 and group 2 consists of PMM 37 and check variety Hara Madhu with approximately 74.00% similarity. Sub-cluster IB comprised two genotypes PMM 32 and PMM 18 with approximately 70.90% similarity among themselves.