Centaurea borysthenica is a local endemic of Ukraine. The phylogenetic position, evolutionary history, and taxonomic status of this controversial species were clarified. The independent status of Centaurea borysthenica as a part of C. arenaria agg. was recognized based on molecular phylogenetic analysis of nuclear (ITS1-5.8S rRNA-ITS2) and chloroplast (rpl32-trnL) sequences of four populations (including two from locus classicus). The species-specific features of C. borysthenica were updated. We recognize the hybridogenic origin of C. borysthenica from C. arenaria agg. (maternal genotype), and a hypothetical species with a unique endemic Eastern European ribotype (paternal genotype). The haplotype of all studied populations was identical to haplotype of C. arenaria and C. odessana that differs from all known haplotypes of C. stoebe s.l. By ribotype, C. borysthenica is an alloploid with a combination of two ITS alleles, one of them belongs to the so-called Balkan ribotype inherent of C. arenaria and C. odessana (reference sequence MW383495), the other belongs to the unique so-called Ukrainian ribotype 3 (reference sequence MW383493 with substitutions 83.Y>C, 458.Y>T). The studied specimens with the phenotype «C. borysthenica» from four populations of Zaporizhzhya, Mykolaiv, and Dnipropetrovsk regions were recognized as secondary hybrids between C. borysthenica and different species of the Centaurea section (especially C. diffusa and C. stoebe s.l.). All these secondary hybrids retain the C. borysthenica haplotype, and the ribotype contains at least one of the alleles of this species is either Balkan or Eastern Ukrainian (the so-called Ukrainian ribotype 3).