In wheat, anthocyanin pigments can be accumulated in pericarp tissues (under control of the Pp genes) resulting in purple-colored grain. In the current study, a strategy, based on the use of molecular and morphological markers, was applied to create purple-grained bread wheat cultivars adapted to the West Siberian region. The breeding scheme started from crossing of recipients (elite cultivars and lines) with donor lines carrying dominant alleles of the complementary genes Pp3 and Pp-D1. The F2 hybrids passed three-step marker-assisted selection, and those having dominant Pp-D1Pp-D1Pp3Pp3 genotypes were backcrossed with the recurrent parents. The desired BC1F2-3 progenies were selected using morphological marker, while BC1F3 also passed through field evaluation. At this stage, 120 lines were selected and planted in individual 1 m2 “breeding nursery (BN) plots” for assessment of heading dates, duration of vegetation period, resistance to powdery mildew, stem and leaf rusts, protein and gluten content, as well as productivity. After these investigations, a total of 17 promising anthocyanin-rich purple-grained lines characterized by multiple resistance and having best yield/quality characteristics were finally candidates for selection of commercial cultivars adapted to the West Siberian climate and suitable for functional food production.