Beta casein (CSN2) is the most abundant protein among the casein fractions, representing up to 50-55% of the total casein content. Kappa casein (CSN3) represents about 15% of the whole casein in milk. Both casein fractions are encoded by the CSN2 and CSN3 genes, which are highly polymorphic, and their variability has a significant effect on milk’s sensory and technological properties. This study aimed to develop an efficient and accurate method for detecting genetic variants for the CSN2 locus (exon 7 and 9); to find out the distribution of variants for CSN2 and CSN3 locus in dairy breeds of goats bred in the Czech Republic. Four hundred eight samples were included in the study for CSN2 locus analysis and had 790 samples for CSN3. SNaPshot analysis was used to determine genetic variants. In CSN2, the predominant allele was C1 (0.41), followed by allele A (0.35). For the CSN3 locus in the monitored years, allele B was more dominant (0.50-0.65) than allele A (0.22-0.40). Alleles C, D, F, and G, had a low frequency of occurrence (below 8%). The obtained information on the distribution of alleles for CSN2 and CSN3 could be helpful in breeding programs to maintain biodiversity and improve the production characteristics of dairy breeds of goats included in genetic resources bred in the Czech Republic.