Holoparasitic genera within family Orobanchaceae are characterised by greatly reduced vegetative organs; therefore, seed micromorphology has proved to be a useful complementary taxonomic criterion. Seeds of 160 samples from 54 localities of 26 taxa of the Orobanche and Phelipanche genera occurring in central Europe, specifically from Poland, the Czech Republic, Austria and Slovakia, supplemented by samples from Spain, France and Ukraine, were investigated using scanning electron microscopy. Thirteen quantitative or qualitative morphological characters of seeds were analysed. The following three types of periclinal wall sculpture of seeds were identified: veined and fibrillar in Phelipanche; with oval or elliptic perforations (pitted) in almost all species of Orobanche; with outer periclinal wall smooth, granular or rugged (very rarely visibly pitted), impeding vision of the inner one, occurring only in O. gracilis Sm. and O. coerulescens Stephan in Willd. The influence of different hosts on the features of seeds of eight species is also presented, as well as relationships between seed morphology and taxonomic classification, including problematic taxa. The best diagnostic features include type of ornamentation of the periclinal wall, perforation diameter (in pitted sculpture), fibrillar diameter (in fibrillar sculpture) and width of anticlinal walls. Size and shape of the seeds and cells and the presence of median troughs are variable; however, these features can be helpful when using larger samples. The usefulness of micromorphological studies on seeds of Orobanche and Phelipanche is demonstrated.