Thunberg encountered nine species of Lilium during his visit to Japan in 1776. Of these, L. lancifolium Thunb., L. longiflorum Thunb., L. maculatum Thunb., and L. speciosum Thunb. are all accepted. He also described L. elegans Thunb., a lily that is morphologically similar to L. maculatum. The long-disputed name L. × elegans is confirmed as correctly belonging to the hybrid comprising L. maculatum and L. pensylvanicum Ker Gawl. Thunberg’s working methodology, including that of his illustrators and engravers, is scrutinised concerning the publication of his Japanese lilies. Four lectotypes and a neotype are designated, a full synonymy is listed for L. maculatum and L. × elegans, and keys to the hybrid and its parent species, as well as to the natural varieties within L. maculatum, are provided.