This work aims to characterize the genetic diversity of species, early hybrids, and cultivars using microsatellite simple sequence repeat (SSR) markers, as well as analyze and identify the origin ofHemerocallisspp. early hybrids. For this research, samples were collected from different types of daylily species, early hybrids (known or hypothetically first-generation hybrids fromHemerocallisspecies), foreign, and Lithuanian varieties. An initial screening of SSR primers developed forHemerocallis citrinawas performed, and their suitability for testing other daylily species and hybrids was evaluated. The genetic diversity was assessed with the selected eight-primer set, and molecular SSR profiles were created. Primer SAU00097 is the most informative according to heterozygosity (0.95) and polymorphism information content (PIC) (0.17). The highest heterozygosity was observed in Lithuanian cultivars (0.713), the lowest in species (0.583). Genetic relationships between species show that only fulvous daylilies are separated into a different cluster. The highest variation among genotypes was observed in the species group (18%), while modern cultivars had the slightest variation among genotypes (1%). The putative origin of early hybrids was analyzed using a likelihood heatmap of all genotypes. Results show what species might be used in breeding for early hybrids. Several modern diploid and tetraploid daylily cultivars have triploid species as ancestors.