Abstract: The genus Avena L. includes cultivated species of great practical importance, segetal weeds, and wild species, which are interesting as potential sources of valuable traits for breeding purposes. Until now, there has been considerable disagreement in understanding the size of the genus, especially regarding the isolation of rare specialized species from aggregate species. The review focuses on the analysis of the authors’ and published data on comparative genomics and taxonomy of species of the genus and discusses the use of different genetic markers in molecular genetic studies for identifying oat species. Modern studies of the genus are largely based on molecular phylogenetic and karyological data. In particular, many studies are focused on the relationships between the only perennial tetraploid species A. macrostachya and diploid species of the genus Avena. This article examines the relationships between the genome of this unique autotetraploid species, formed before the evolutionary division of the genus into separate genomes, and the A and C genomes of other species. On the other hand, oats are well studied with respect to agronomic and economically important traits using traditional field and laboratory methods. Molecular markers are often used to isolate the sources of biotic stress tolerance. The selection of oat genotypes characterized by disease resistance, in particular, to fusarium infection and the accumulation of mycotoxin deoxynivalenol (DON) in grain, is carried out using quantitative trait loci (QTLs) mapping strategy. QTLs that controlled resistance to mycotoxin accumulation were identified. In addition, QTLs were detected that, with an increase in the length of the growing season and plant height, decreased the accumulation of DON mycotoxin in the oat kernel. The use of marker-assisted selection (MAS) for the identification of genotypes resistant to the most important diseases of oats and for other breeding traits is discussed. Modern approaches to genotyping of breeding important traits are considered.