Çatalburun (Fork-nose) dogs are the members of Turkey›s indigenous gene pool. Although there are some studies on phenotypic identification of this breed, there is no study on genetic characterization. This study aimed to define the detailed morphological and genetic characteristics of this breed. For this purpose, initially, some morphological traits in 100 Çatalburun dogs were measured. Furthermore, the blood samples were taken from a total of 62 animals to identify genetic characteristics. The mean live weight was found as 20.20 kg, and the means of withers height, rump height and body length were measured as 48.2, 49.1 and 54.1 cm, respectively. In the microsatellite analysis, the mean of inbreeding coefficient (FIS) was calculated as 0.048. The observed (Ho) and the expected heterozygosity (He) values were determined as 0.743 ± 0.12 and 0.744 ± 0.11, respectively. Mitochondrial DNA (mtDNA) sequence analyses revealed that AHT 137 loci (12 alleles) and REN247M2 loci (4 alleles) were found to have the highest and the lowest frequencies. The highest frequencies in A and B haplogroups were found to be A18 (14.52%) and B1 (59.68%) haplotypes, respectively. The factorial similarity analysis denoted that the examined dogs may be grouped in closely-related two parent lines. Although the heterozygosity values were found to be relatively high, conversely, the mutation or nucleotide diversities were found to be low. This is the first study to comprehensively describe the genomic diversity and population structure of the Çatalburun breed. Special attentions should be taken to the protection of this breed as soon as possible.