Three molecular markering techniques: inter-simple sequence repeat (ISSR); start codon targeted (SCoT), conserved DNA-derived polymorphism (CDDP) markers were compared for fingerprinting of 40 varieties of bread wheat. The number of scoreable and polymorphic bands produced using the ISSR, SCoT and CDDP primers for varieties was more than that of genotypes. Average polymorphism information content (PIC) for ISSR, SCoT and CDDP markers was 0.39, 0.41 and 0.34, respectively, and this revealed that three different marker types were equal for the assessment of diversity amongst genotypes. Cluster analysis for three different molecular types revealed that genotypes taken for the analysis can be divided in three and four distinct clusters. There were no significant differences among these markers in terms of the evaluation of genotypes. These results suggest that efficiency of SCoT, CDDP and ISSR markers was relatively the same in fingerprinting of genotypes but SCoT and CDDP analysis are more effective in fingerprinting of wheat genotypes. To our knowledge, this was the first detailed report of a comparison of performance among two targeted DNA region molecular markers (SCoT and CDDP) in comparision with ISSR technique on a set of samples of wheat cultivars. Overall, our results indicate that SCoT, ISSR and CDDP fingerprinting could be used to detect polymorphism for genotypes of wheat.