The present investigation evaluated genetic diversity of 42 wheat cultivars and advanced breeding lines using morphological, biochemical and molecular markers (ISSRs). The clustering pattern based on phenotypic data using WARD method assigned the wheat genotypes into seven groups. The 17 ISSR primers amplified a total of 114 alleles of which 95 alleles (83.34%) were polymorphic. The majority of the primers showed PIC value close to the average (0.68–0.74), while EMR feature varied from 2 to 14 with a mean value of 4.8. The MI values ranged between 1.36 and 12.64. The primers that showed higher polymorphism had higher EMR and MI values. The estimates of RP ranged from 0.90 to 6.67 with an average of 2.55. The genotyping data of the ISSR markers were used to assess genetic variation in the wheat accessions by UPGMA-based dendrogram and principal coordinate analysis (PCoA). Both of the methods classified the 42 wheat accessions in seven groups and presented similar grouping of the genotypes with some minor deviations.