Intraracial differences in the Carpathian honeybee race Apis mellifera carpatica from Russia and Tajikistan with the race standard (Vuchkovski line from Transcarpathian oblast of Ukraine) are compared by morphometric and molecular-genetic study. The most informative features, the “cubital index” and the “discal displacement,” are shown to deviate significantly from the standard. However, the calculated genetic distance between datasets from different regions indicates the uniformity of the Carpathian race across its distribution range. The nucleotide composition of the mtDNA COI gene (1535 bp) reveals two groups of haplotypes associated with the apiary foundation time and differing by the amino acid composition of the COI protein (group I, asparagine; group II, serine). In addition to honeybee samples from different regions, group I includes honeybees from an isolated apiary in the mountain-forest zone of Crimea, which originated from the honeybee line 77 from the Transcarpathian. Group II includes honeybee samples of the modern “Vuchkovski” standard line.