Common wheat ( Triticum aestivum L.) is the most commonly grown cereal in the world. In this time wheat genotypes with different colour of kernels have become more important not only to enhance food sources, but also for its importance as a function food, which provides health-promoting substances. Anthocyanins, flavonoid substances in nature, are responsible for the different pigmented caryopsis of common wheat. Pigments formed in anthocyanin biosynthetic pathway are stored in different parts of the caryopsis. Purple pigments are accumulated in the pericarp and blue pigments are accumulated in the aleurone layer of the caryopsis. In this work we use spring forms of common wheat with white endosperm (Novosibirskaya 67), with purple pericarp (ANK - 28B and Abissinskaya Arraseita), and with blue aleurone layer (UC66049 and Tschermaks Blaukörniger Sommerweizen) from Agrotest fyto Kroměříž, s.r.o. collection. Total RNA from this genotypes was isolated using a phenol-chloroform extraction. Total RNA was transcribed into cDNA by reverse transcription. Based on the obtained PCR products sequences were obtained candidate gene sequences for dihydroflavonol-4-reductase (95-100% similarity) and anthocyanidinsynthase (90% similarity). The variability among genotypes in this study was due to single nucleotide polymorphisms and indels. The obtained candidate sequences were localized in the wheat genome and after that was studied gene expression of DFR gene by using qPCR.