Tulipa (tulips; Liliaceae) is a genus of geophytes comprising c. 76 species, occurring from southwestern Europe and North Africa to Central Asia. The taxonomy and classification of the genus have been contentious in the past. We investigated the phylogenetic relationships in the genus using DNA sequences from five plastid regions (trnL intron and trnL–trnF spacer, rpl16 intron, rps12–rpl20 intergenic spacer and matK) and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. Amana and Erythronium were used as outgroups. Sequences were obtained from 25 Tulipa taxa representing all major lineages previously identified as distinct and four outgroups (two Amana spp. and two Erythronium spp.). In the combined maximum parsimony analysis, Tulipa was strongly supported as monophyletic and four clearly defined clades in the genus were obtained, although the relationships between them were unclear. In support of previous molecular studies, the results suggest that section Clusianae should be excluded from subgenus Tulipa and accepted at subgeneric rank. Subgenus Eriostemones and subgenus Tulipa (excluding Clusianae) were both strongly supported. Tulipa sprengeri, traditionally placed in subgenus Tulipa, was shown to be a member of Eriostemones. Orithyia, in this study represented by T. uniflora, formed a fourth lineage, also to be treated at subgeneric level. In the Bayesian analysis, the genus Tulipa was strongly supported and the same four lineages (subgenera) were identified. In this case, Orithyia was sister to the rest of the genus (with moderate support) and subgenera Clusianae and Eriostemones together formed a clade with strong support. Original species descriptions and type specimens of as many names as possible were reviewed and, on this basis, a revised checklist with full synonymy, typification and distribution is provided. The status of T. ×gesneriana and its synonyms is discussed. All accepted species are classified into the four subgenera supported by our phylogenetic study.