The origin of diploid C-genome oat Avena bruhnsiana, which is a rare endemic species from Azerbaijan (Apsheron Peninsula) has been clarified. This diploid oat was found only in Apsheron Peninsula in Azerbaijan and is closely related to another diploid species, A. ventricosa that belongs to C-genome oat group. In culture these species form fertile progeny but do not cross with other C-genome oats, A. clauda and A. pilosa. For more precise phylogenetic picture we used the next-generation sequence method that allows to obtain the whole pool of marker sequences (in our case, 18S rDNA(fragment)–ITS1–5.8S rDNA). Based on NGS counts, we revealed that at least 67% of A. bruhnsiana rDNA were received from A. ventricosa. The second ancestor of A. bruhnsiana is probably A. clauda. Avena clauda itself appears to be a homoploid hybrid: one of its main ribotypes is identical to A. pilosa and one of them is separate. Also, one of the minor ribotypes of A. pilosa is related to A-genomes (probably, ancestral state?). The only tetraploid in the genus, perennial A. macrostachya, has CmCm-genome and was also studied in our work. It takes distant position among other C-genome oats having two closely related main ribotypes. Avena macrostachya ribotypes is connected only with A. clauda/A. pilosa complex via minor ribotype fraction.