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AbstractThe aim of this work was to assess the interaction between MC1Rand ASIPgenes in determining coat colour variation in black and brown Peruvian alpacas. Skin biopsies were collected from 25 black alpacas and 15 brown alpacas. Genomic DNA was isolated, amplified and sequenced. Black alpacas were dominant homozygous (E/E)or heterozygous (E/e) at MC1Rlocus while brown alpacas were heterozygous at the locus. All the black animals were heterozygous for the non-functional alleles at ASIP locus (aH– aΔ57– aht). On the contrary, brown alpacas were dominant homozygous (A/A) or heterozygous (A/aht) at this locus. When the combined genotypes at MC1Rand ASIPwere considered together, alpacas with black coats had four possible genotype combinations namely aH/aΔ57– E/E, aH/aht– E/E, aH/aΔ57– E/eand aH/aht– E/e. The brown alpacas were found to have the A/aht– E/eand the A/A – E/egenotype. Our results show that the two genes interact to sinergically modulate the amount of melanin synthetised in alpaca fibre. In black coat alpacas in fact, the expression of non-functional ASIP results in the failure of pheomelanin production while the functional MC1R allows the synthesis almost exclusively of eumelanin. On the other hand, the brown coat phenotype is produced when the animal possesses at least one functional copy of the gene at both ASIPand MC1Rloci. In fact, MC1R binds both ASIP and α-MSH allowing a mixed melanogenesis characterised by the synthesis of eumelanin and pheomelanin granules in a similar ratio.HIGHLIGHTSThe income of thousands of Peruvian alpaca farmers depends mainly on the sale of fibre in high demand on the global textile market.A wide variety of colours exists, therefore this fibre is preferred by the ecologically sustainable industry for organic textile products.Our results provide information for selection breeding program of coloured alpaca helpful to improve the condition of welfare of Andean populations.