Genes for adaptation to climatic conditions can have an impact on the expression of genes for agricultural productivity. This study tested the hypothesis that winter wheat cultivars registered in middle Europe (especially the Czech and Slovak Republics) during the period 1976–2009 were differentially adapted to different regions, reflecting selection for different allelic combinations. This was tested by analysing for the presence of alleles at the Rht and Ppd loci using molecular markers and gibberellic acids (GA) response tests. Four allelic variants (174, 192, 165 and 198-bp) were detected at the Xgwm261 locus linked to Rht8 on chromosome 2D. The 198-bp allele was rare, but present in some of the most widely grown cultivars. Of 85 cultivars grown in the area of Czech Republic, the 174-bp allele predominated in frequency and area (39 cultivars), often in combination with Ppd-D1b (30 out of 39 cultivars) and Rht-D1b (15 out of 30 cultivars). In neighbouring Slovakia, the 192-bp allele, generally associated with Ppd-D1a, was detected in 30 out of 40 cultivars; in 12 cultivars accompanied by a GA-insensitive allele on 4B chromosome (pedigree analyses indicated a high prevalence of the Rht-B1d allele). The 192-bp (Rht8)/Ppd-D1a linkage block was broken up in 7 out of 22 cultivars that carried the 192-bp allele in the ‘Czech collection’. Analysis of the effects of year of registration on allele frequency showed a decline in GA-insensitive cultivars released recently in both countries, and great changes in the frequency of the 2D alleles during the period 1981–2009 in the Czech Republic. The pedigrees of successful cultivars were examined to find probable sources of Xgwm261 192-bp, 174-bp and 165-bp alleles on 2D and Rht genes located on chromosomes 4B and 4D. These results will impact on breeding strategies and the exploitation of existing registered wheat cultivars in different regions and growing systems.