Genetic studies on pre-Hispanic populations of the Southern Andes have been increasing steadily in the last decade. Nevertheless, ancient DNA characterization of Formative Period archaeological human remains is particularly scant, especially for Northwest Argentina. In order to enlarge current information on genetic characterization of the first agricultural communities of the Southern Calchaquí Valleys, we present and discuss the first mitochondrial aDNA information obtained on samples dated to ca. 3600-1900 years BP from the Cajón Valley, Catamarca Province. Reproducible mtDNA HVR-1 sequences were obtained in 7 individuals. Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups D1 (57.1%), C1 (28.5%) and B2 (14.2%), with absence of A2.