The modern concept of the species as a complex biological system is ba
sed on the work of N.I. Vavilov, who was the first to emphasize the po
tential of a species for breeding. Realization of his ideas became pos
sible only in the era of modern biology, with the advent of the latest
biological methods of genetic and phylogenetic analysis of plants. Am
ong these methods are molecular marking of genetic systems and biologi
cal structures with highly informative molecules of proteins and nucle
ic acids. These techniques are used to identify species, varieties, an
d biotypes; detect hidden variation in populations; analyze the genome
, and estimate interspecies genomic relationships in allopolyploid pla
nt complexes. Genomic and genetic studies of principal species of cult
ivated plants and their wild relatives have shown that the nuclear gen
ome may be regarded as a genetic system of species category. The role
of genetic variation in evolution and breeding; the genetic structure
of species and its use for breeding; and the importance of cultivar, s
pecies, and superspecies gene pool levels for determination of genetic
ally and morphogenetically complex plant traits are discussed.