Determining the genetic polymorphism is essential for evaluating the outcomes of breeding programs. Thus, the current study aimed at comparing two methods to measure the genetic polymorphism of the cairo-mix broiler hybrid, this was done by using 100 genomic DNA samples.  The microsatellite marker method and the start codons targeted (SCoT) marker techniques were used. The results showed that 14 microsatellite loci detected 34 alleles with an average of 2.43 alleles per microsatellite. While ten SCoT loci detected 66 alleles with an average of 6.6 alleles per primer. The effective number of alleles for the microsatellite markers ranged from 1.47 to 2.77 (mcw0217 and adl0266), whereas for SCoT markers, it ranged from 2.38 to 5.55 (SCoT-18 and SCoT-1). Moreover, among the SCoT markers, SCoT-01, SCoT-10, SCoT-40, SCoT-44, and SCoT-50, primers were found to be the most informative and discriminative. The averages of shannon's information index were 0.82 and 1.64 for the microsatellite and SCoT markers, respectively. The mean values of observed heterozygosity were 0.77 and 1.00 for the microsatellite and SCoT markers, respectively. In conclusion, the high genetic diversity of the cairo-mix hybrid indicates that promising results may be expected in future breeding programs. The SCoT markers as a simple and informative technique could be a potent method for studying genetic variation in poultry.