Abstract   The daylily (Hemerocallis spp.) is one of the most economically important ornamental plant species in commerce. Interestingly, it is also one of the most heavily bred crops during the past 60 years. Since the American Hemerocallis Society began acting as the official registry of daylily cultivars in 1947, more than 40 000 registrations have been processed. In order to determine the effects of intensive breeding on cultivar development, and to study relationships among different species, genetic variation in the daylily was estimated using AFLP markers. Nineteen primary genotypes (species and early cultivars) and 100 modern cultivars from different time periods were evaluated using 152 unambiguous bands (average 79% polymorphism rate) derived from three AFLP primer combinations. Overall, pairwise similarity estimates between entries ranged between 0.618 and 0.926 (average=0.800). When comparing cultivar groups from different time periods (1940–1998), genetic similarity was initially increased, compared to the primary diploid genotypes, remained constant from 1940 to 1980, and then steadily increased as breeding efforts intensified and hybridizers began focusing on a limited tetraploid germplasm pool derived by colchicine conversion. Among modern (1991–1998) daylily cultivars, genetic similarity has increased by approximately 10% compared to the primary genotypes. These data were also used to evaluate recent taxonomic classifications among daylily species which, with a few minor exceptions, were generally supported by the AFLP data.