Resistant varieties allow to reduce water consumption, application of pesticides and herbicides during their production, which is necessary for the development of energy-efficient and organic cultivation technologies. Another task facing breeders is the creation of black-grain and red-grain rice varieties containing up to 20 times more antioxidants than white-grain rice varieties for functional nutrition. To solve these problems, systems of molecular markers have been developed to control the inclusion of target loci in the cultivar genotype. The production of rice varieties with colored pericarp in Russia is associated with the inclusion in the genotype of created varieties genes that determine drought resistance, due to the lack of irrigation water in most rice-growing regions. To reduce the complexity of creating varieties of functional direction with given characteristics, markers linked to genes of interest are grouped into multiplex complexes presented in the work. They simultaneously control both the adaptability and the nutritional value of the material. Four multiplex complexes control 11 loci that determine the content of micro and macro elements. The first one controls the genes that determine the content of Mn, Ca on chromosome 3 and Zn on the eighth chromosome. The second controls two genes that determine the content of iron (on chromosomes 6 and 8) and manganese on the tenth chromosome. The third helps to identify polymorphism at the loci that determine the content of Zn, P, K and other traits that determine the nutritional value on chromosomes 5, 6, 8. Five complexes help to track the inclusion in the genotype of 13 loci that determine the formation of traits associated with the adaptability of rice samples.