Mitochondrial DNA (mtDNA) cytochrome b gene sequences were utilized to assess the genetic diversity and phylogenetic relationships of non-descript and Hyla rabbit populations in Nsukka, Nigeria. Non-descript rabbits, as locally adapted genotypes, play a crucial role in preserving genetic diversity and adaptability. Our analysis revealed both non-descript and Hyla rabbits as polymorphic, with non-descript rabbits exhibiting higher haplotype diversity (0.761±0.092) compared to Hyla (0.598±0.032). Nucleotide diversity ranged from 0.10137±0.00021 in non-descript to 0.06405±0.01057 in Hyla, underlining the genetic variation and adaptability of non-descript rabbits. The significantly negative Tajima's D value (-1.53783) in non- descript rabbits indicates natural selection and rare allelic combinations, further highlighting their unique genetic signature. Phylogenetic analysis unveiled two distinct clusters, with Hyla, New Zealand, and Californian rabbits forming one group and non-descript, Chinchilla, and Domestic English rabbits comprising the other. This suggests a history of genetic exchange and hybridization, particularly with Hyla possibly being a result of crossbreeding between Californian and New Zealand white rabbits. The genetic distinctiveness of non-descript rabbits reinforces their potential role in maintaining indigenous genetic
resources. To harness the genetic potential of these rabbit populations, we recommend comprehensive genetic characterization incorporating nuclear DNA markers and quantitative traits. Breeding programs should prioritize the preservation and improvement of locally adapted genotypes, and efforts to conserve and utilize Animal Genetic Resources (AnGR) should focus on preserving unique genetic variants found in non-descript rabbits, thereby, addressing food security and promoting environmental sustainability in livestock production in Nigeria.