The alpaca is of greatest economic importance in the Peruvian High Andes. This study aimed to determine the genetic diversity of three Peruvian alpaca farms, as well as, to validate a microsatellite markers panel for paternity testing. In this study, 247 samples of Huacaya alpacas were taken from three different localities (Sanjo, San Pedro de Raco and Cachipampa) from Pasco Region in Peru. DNA was obtained from hair follicles and genotyped for 15 microsatellites markers in multiplex electrophoresis runs.A total of 225 alleles were detected across the 15 loci investigated. The polymorphism information content considering all loci was 0.82, which indicated that the microsatellite panel was very polymorphic and highly informative. The estimated diversity parameter showed that farms have high levels of genetic diversity (HE = 0.826), and revealed the existence of genetic differentiation...