White Short-Haired (WSH) and Brown Short-Haired (BSH) are two protected local goat dairy breeds in Czech Republic. A genetic characterization of both breeds is necessary to preserve them from extinction and to exploit their genetic variation. For this purpose a study was carried out on the genetic polymorphism of the CSN2 and CSN3 loci. Genomic analysis was performed by PCR method. Both breeds were characterized by the absence of CSN20 allele. The CSN3 locus was found polymorphic, with the CSN3A, CSN3B and CSN3C alleles frequency of 0.15, 0.80 and 0.05 in WSH and 0.52, 0.40 and 0.08 in BSH, respectively.