Boreal Lilium distichum and temperate L. tsingtauense are morphologically very similar, thus they have been placed in the section Martagon. Recent molecular phylogenetic analyses revealed that L. distichum and L. tsingtauense are indeed the most closely related species within that section. Lilium distichum has a wider geographic range and a broader niche than L. tsingtauense. We hypothesized that L. distichum— L. tsingtauense might be a classical “progenitor—derivative” (P–D) species pair and examined the levels of allozyme diversity in the two species in South Korea. Whereas the allelic composition of L. tsingtauense represented a subset of L. distichum, the former had significantly lower allozyme variability at both the population and the species levels than the latter. Except for the locus Fe (fluorescent esterase), allele frequencies of L. distichum were very similar to those of L. tsingtauense. Accordingly, pairwise genetic identities between populations of L. distichum and L. tsingtauense were very high, with a mean of 0.919. Our allozyme results support the hypothesis that L. tsingtauense is a derivative species of the progenitor L. distichum.