Perennial ryegrass (Lolium perenne L.), an important forage grass species in temperate regions, is genetically improved by population breeding. Although valued for their broad genetic base, the resulting synthetic varieties only partially exploit heterosis. Hybrid breeding offers opportunities to fix beneficial heterotic patterns more effectively and, hence, to increase the yield potential. A suspected bottleneck in the production of perennial ryegrass hybrids is the genetic intermixture of existing germplasm, impeding the definition of heterotic groups. In this study, selected parental populations of a diploid and tetraploid cytoplasmic male sterility (CMS)-based hybrid breeding program were characterized using genotyping-by-sequencing (GBS). Hybrid populations, derived from 26 parental combinations of the tetraploid breeding program, were tested for yield performance and compared to synthetic varieties at five sites over four growing seasons. The hybrids significantly outperformed the synthetics by 4.15% on average for total dry matter yield. Additionally, GBS revealed the existence of sub-populations within the tetraploid CMS germplasm. This sub-population structure represents the untapped potential that could be exploited for heterosis to further increase biomass yields. Here, we show that CMS hybrids generate substantial yield gains in perennial ryegrass and provide a method to further improve hybrid breeding, using GBS to select for heterotic groups.