Abstract <p>The Krasnodar wheat and triticale breeding school is one of the oldest in Russia. Over a century of research and breeding at the National Grain Center, about 300 wheat cultivars have been developed, many of which have been widely cultivated both domestically and internationally and actively used in breeding programs. Currently, 124 of these cultivars are registered and approved for commercial use. One of the critical challenges in wheat breeding programs is the identification of optimal allelic combinations of genes controlling the main agronomic traits. However, the allelic composition of recently identified genes or novel allelic variants of known genes affecting productivity and adaptability remains poorly characterized in commercially successful cultivars. The Lukyanenko National Grain Center (NGC) plays a leading role in Russia in developing highly demanded cultivars, including a novel crop—winter durum wheat. Genes involved in winter and frost resistance play a special role for Krasnodar krai. In this study, we conducted a molecular genetic analysis of a collection of bread and durum wheat cultivars developed by the Wheat and Triticale Breeding and Seed Production Department of the Lukyanenko NGC. The distribution of allelic variants was assessed for genes associated with plant height (<i>Rht-B1</i>, <i>Rht-D1</i>), regulation of the transition to flowering (<i>Vrn-A1</i>, <i>Ppd-A1</i>, <i>Ppd-D1</i>), frost resistance (<i>Fr-A2</i>), and grain size (<i>GW2</i>, <i>NLP3-B1</i>, <i>TaGS2-A1</i>), as well as for the presence of wheat–rye translocations (1RS.1BL, 1RS.1AL). The results of the study demonstrate the features of the allelic landscape in the most commercially successful varieties of bread and durum wheat bred by the Lukyanenko National Grain Center.</p>