A set of 43 microsatellite loci was used to characterise the malting barley varieties and breeding lines used for the Protected Geographical Indication (PGI) “České pivo” (“Czech beer”) and for other beer types. Genotype data were compared with technological malting quality parameters. The analysis of variance showed significant differences between varieties used for the given PGI and varieties used for other beer types in six variables. Three clusters of varieties specific to the PGI and three clusters specific to malting barley genotypes for other beer types were identified using a Bayesian approach. The remaining four clusters expressed effects of parent lines. The discrimination analysis based on malting quality and molecular variables identified only one barley breeding line suitable for the PGI “České pivo”.