Garden beet is the ancestor of fodder beets and sugar beets, but the origin of garden beet's genetic potential to evolve novel beet types is debatable. In this study, we analyzed nuclear and mitochondrial DNAs in 47 garden beet accessions using DNA markers. Multiple analytical methods revealed a unified population structure with subpopulations evident in the European and Caucasian accessions. We diagnosed mitochondrial genome types (mitotypes) based on mitochondrial minisatellite loci in 541 plants from the 47 accessions, revealing a major mitotype and 11 minor mitotypes in garden beets from Europe and the Caucasus region that were also present in endemic leaf beets and wild beets. Our data indicate that European and Caucasian garden beets include genetically differentiated subpopulations. Provided that the occurrence of minor mitotypes is a vestige from crosses with leaf beets and wild beets, the notion that introgression contributed to increasing the genetic diversity in the garden beet gene pool is substantiated at the molecular level.