In this study, the genetic diversity of GNU zebrafish and common zebrafish populations was investigated using PCR-RFLP method. For enzymatic digestion of PCR product, 5 restriction enzymes AluI, DpnI, Eco47I, HindIII HinfI were used. Data analysis was performed using Arlequin 3.11 software. As a result of these analyzes, 12 different haplotypes were obtained, of which 9 haplotypes were related to GNU zebrafish and 3 haplotypes were related to normal zebrafish. In normal zebrafish, AAAAA haplotype was the most abundant and in Gnu zebrafish, EABAB, EACAB and CABAB haplotypes showed the highest frequency. Calculation of haplotypic and nucleotide diversity showed that the diversity in the mitochondrial genome of GNU zebrafish is higher than that of normal zebrafish. Studies on the resulting genotypes showed that PCR-RFLP is a suitable technique for determining genetic diversity between the two species of fish.