Genetic diversity in rabbit populations plays a critical role in breeding programs aimed at enhancing desirable traits. This study investigates allele diversity at microsatellite loci in Baladi Black and New Zealand White rabbit breeds, as well as their crossbred offspring. Genome scanning using 6 microsatellite markers was applied to genotype animals. The results revealed that allele counts in Baladi Black rabbits varied markedly among loci, ranging from 4 to 13 alleles per locus with an average of 7.33. Effective allele numbers (Ne) showed similar variability, ranging from 2.07 to 10.1. Contrasts between observed (No) and effective alleles (Ne) indicated varying degrees of genetic activity, with differences ranging from 0.7 to 3.9 across loci. New Zealand White rabbits displayed a range of 4 to 15 alleles per locus, with effective allele numbers from 2.81 to 13. Differences between No and Ne ranged from 0.9 to 2.9. Crossbred rabbits exhibited intermediate allele counts (average 5.66 alleles per locus) and effective allele numbers (ranging from 1.69 to 8.1), reflecting genetic contributions from both parental breeds. Heterozygosity analysis revealed moderate to high observed (Ho) and expected (He) heterozygosity levels across populations. Polymorphic Information Content (PIC) values indicated moderate to high levels of polymorphism, with Baladi Black and New Zealand White breeds averaging 0.720 and 0.758, respectively, and crossbreds averaging 0.641 across loci. These findings underscore the multi-allelic nature of microsatellite loci and highlight their utility in assessing and enhancing genetic diversity in rabbit populations, essential for sustainable breeding and conservation strategies.