Kuri cattle of the Lake Chad Basin represent a geographically restricted African cattle population characterised by ecological adaptation and a complex taurine–zebu genomic background. The present study aimed to characterise variation in selected functional nuclear genes together with mitochondrial DNA diversity in eight Kuri cattle individuals (n = 8), including six bulls and two cows. A fragment of the mitochondrial D-loop region was sequenced to assess maternal lineage diversity, while nuclear loci associated with milk protein composition (CSN2, CSN3, CSN1S1, CSN1S2, LGB), lipid metabolism (DGAT1), and thermoregulation (PRLR/SLICK locus) were analysed using PCR and Sanger sequencing. Mitochondrial analysis revealed the presence of multiple maternal haplotypes within the examined sample. Nuclear genotyping demonstrated polymorphism at several milk protein loci, including the β-casein gene (CSN2), where both A1 and A2 alleles were detected. The DGAT1 locus also showed allelic variation, whereas the analysed SLICK-associated region was monomorphic in all individuals. Although based on a limited number of animals, the results indicate the persistence of functional genetic variability in this locally adapted cattle population and provide baseline molecular data for future conservation and breeding studies.