Alpaca (Lama pacos) is a domesticated South American camelid mainly distributed in Peru, although also present in Bolivia, Chile and Ecuador. This species, highly appreciated because of its lustrous and silky natural fibre, has been poorly studied at the genetic level. Characterisation of the genetic diversity of alpaca would be fundamental for gaining new insights into past domestication events as well as for understanding the demographic history of this species. In the present work, we report the mitochondrial genetic variability of alpacas (n=29) distributed in eight farming areas of the south region of Peru. Sequencing of the D-loop region revealed the existence of 16 haplotypes. Haplotype (Hd) and nucleotide (π) diversities reached values of 0.96 and 0.0456, respectively. Moreover, analysis of the cytochrome b region evidenced the segregation of 15 haplotypes (Hd = 0.946, π = 0.0279). We can conclude that, despite the drastic reduction in the census of alpacas, there is still a considerable level of genetic variation. Median-joining network and neighbour joining phylogenetic analyses showed the existence of two guanaco-like and vicuiia-like mitochondrial haplogroups. These results might be explained by the occurrence of ancient hybridisation events between llamas and alpacas with the goal of recovering the alpaca population that was decimated by the Spanish colonisers two centuries ago.