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Unigene sequence tagged microsatellite markers were used to analyze the genetic diversity among 30 sugarcane clones with different genetic background to identify diverse parents for utilizing in crossing program. Jaccards similarity co-efficient value based on the molecular marker indicated that eight new ISH and IGH clones viz., IA 1504, SSCD 941, N1 0107, 98 N1 1305, 98 N1 1303, GU 07-291, SSCD 1755 and SSCD 682 had low genetic similarity with commonly used parents. Genetic similarity coefficient and clustering of genotypes were worked out utilizing UPGMA method and the highest genetic similarity was observed between CoC 671 and Co 88025 (0.94) wherein Co 88025 was the somaclone of CoC 671. This demonstrated the efficiency of these molecular markers to differentiate even very closely related individuals. The lowest similarity was observed between ISH 100 and 9870101 (0.42) followed by 87 A 380 and ISH 100 (0.42). Clustering based on genetic similarity coefficient values grouped the genotypes into 8 distinct clusters. A total of 14 diverse parental combinations were identified and their utilization in crossing program is discussed. In addition, four clones viz., 87 A 380, IA 1504, ISH 100, N1 0107 were identified by the presence of specific markers which will be helpful in identification of true hybrids when these clones are involved in hybridization programme.