The selected cytochrome c oxidase subunit I (COX1) gene, and four microsatellite markers were used to investigate the population genetic structure of Red Baladi (RB), and Sinai Gabali (SG) rabbits as the Egyptian native rabbit breeds. Additionally, genetic assorted variety of these breeds was contemplated by utilizing both microsatellite markers and COI gene as DNA standardized identification barcode. A total of 50 does (25 animal for each breed) were used. Live body weight measured at 17 months of age, also the blood samples were collected for molecular analysis. Four microsatellite markers (SAT3, SAT13, SOL33, and SOL44) were used. A total of 18 alleles were discovered across the breeds. the range of alleles per locus discovered over loci and breeds was 3.63 ±0.26 alleles. All microsatellite markers were polymorphic, and the average polymorphic information content (PIC) was 53%. The mean of He values were 0.67±0.06, and 0.74±0.1 for SG, and RB, respectively. The Ho for different markers averaged 0.7±0.06 and ranged from 0.52 at marker SOL33 to 0.90 at markers SAT4. The overall mean of He was 0.574±0.04, and ranged from 0.45 at SOL33 to 0.69 at SAT4.  Among the four loci, the hardy Hardy-Weinberg equilibrium was highly significant (P≥0.001) for both of RB and SG for SOL44 locus. Although SOL33 locus was highly significant for SG, but it was not significant for RB. The highest reduction in heterozygosity (F_ST) values varied from 0.008 (SAT13) to 0.27 (SOL44). Concerning live body weight, there was a highly significant difference in live body weight between RB and SG (P≥0.001), where the difference in body weight between RB and SG was 419±83.3, the least square means were 3188 ± 47.1, and 2768 ± 68.7 for RB and SG breeds, respectively. In the present study, the similarity percentage between sequence reads for RB and SG breeds were 99%. At a starting codon 3, the RB has 227 amino acid, and the SG has 226 amino acid. Moreover, two single nucleotide polymorphisms have detected (SNP: C>A, and G>A) located at 273, and 275bp. There was a significantly association between the enclosed C>A SNP with BW. In addition, the general linear model analysis showed significant association between the live body weight and SAT4 locus (P≥ 0.05).

From the present study, both microsatellite and the COI gene as a DNA barcode had proved to be exceedingly successful in distinguishing between breeds under investigation and genetic assorted variety between them.