The genus Pinguicula (Lentibulariaceae) is unusual within the dicot order Lamiales because of the occurrence of both embryos with two cotyledons and those with just one cotyledon. In order to elucidate the infrageneric relationships and the evolutionary history of the embryo, we analysed (1) the internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (nrITS) of 29 Old and New World taxa of Pinguicula, and (2) the morphological and anatomical characters of the seeds. We suggest that the cotyledon number and spermoderm structure were quite unstable in the evolution of Pinguicula. Although basal nodes of the nrITS tree are sensitive to taxon sampling, all tree topologies found in this study imply homoplasy in the cotyledon number.