The present study aimed to investigate molecular sex differences between males and females of two members of family Cyprinidae in Egypt namely Benni and Lebeis using two different molecular markers i.e., start codon targeted polymorphism (SCoT) and inter simple sequence repeats (ISSR). The bulked DNA sample for each gender of the tested species was screened with eight primers from each marker. However, SCoT marker was more efficient than ISSR marker by showing higher number of possible sex-specific bands in the two tested species. SCoT primers were able to generate 7 and 4 male-specific bands, along with two and 5 female-specific bands for B. bynni and L. niloticus, respectively. Whereas, ISSR primers generated 4 and two male-specific bands, vis-à-vis two and three female-specific bands for B. bynni and L. niloticus, respectively. Interestingly, SCoT-01 primer generated unique common female specific band (690bp) which appeared only in the females of Benni and Lebeis. This band is more possible to be female sex-specific. The results obtained in this study could serve as a keystone for molecular sex differentiation studies in the two tested species and other fish species. However, increasing the number of analyzed individuals is highly recommended.