Skatole and androstenone and their accumulation in fat are the main molecular compounds causing the unpleasant boar taint of porcine meat. This research focused on the variability of genotypes in two genetic markers associated with skatole (CYP2E1) and androstenone (TEAD3) levels in boars of five breeds in the Czech Republic. Differences in genotypes and allele frequencies provide important information and the possibility of genomic selection of makers associated with boar taint compounds.