Phylogenetic relationships within the orchid genus Pleione were reconstructed using maximum parsimony analyses of plastid and nuclear DNA and morphology for 20 taxa to evaluate infrageneric groups, controversial species delimitations, and parentage of several putative wild hybrids. Separate analyses of each data set produced mainly congruent clades when P. × confusa and the Chinese accession of P. hookeriana were excluded. Analysis of the combined data indicated that traditional divisions of the genus into various subgenera and sections are supported when they are based on apomorphic characters. Sections found to be paraphyletic appear to be based on homoplasious and plesiomorphic characters. For an infrageneric classification of Pleione based on phylogenetic relationships three groups are suggested. Taxa within the P. bulbocodioides complex do not show much molecular divergence. Pleione maculata and P. praecox are proposed to be the paternal and maternal parent of P. × lagenaria, respectively, as their nuclear and plastid genomes were almost identical to their natural hybrid. Furthermore, DNA sequences confirm the paternal and maternal parent origin of P. × confusa from P. forrestii and P. albiflora as already suggested by morphological and karyotype data. Molecular data are not conclusive about parentages of P. × taliensis.