The main objective of the current study was to investigate the genetic polymorphism at exons 7 and 9 of the p-casein (CSN2) and exon 4 of the kappa-casein (CSN3) locus in the population of historical Czech goat breeds comprising White and Brown Short-Haired goats. The reliable, sensitive, and reproducible assay PEA in the commercial version of SNaPshot was applied for efficient milk protein genotyping. The genetic polymorphism in the CSN2 locus was determined at 3 years sampled (2008-2022), and in the CSN3 locus at 5 years (2011-2022). We analyzed 543 animals from the genetic resources program for the variants of CSN2 (A. C, Cl, and null alleles). The development of allelic frequencies showed that the A allele increased from 35% to 37%. On the contrary, there was a significant decrease in the occurrence of the C allele group (C + Cl) from 68% to 14.51% +48.39%, respectively. However, we noted an increase in the Cl allele to 48%, an increase in the frequency of the heterozygote AC1 to 37%, and the homozygote Cl Cl to 22% in the monitored goat population.