Seed and fruit morphology of four genera of Orobanchaceae: Cistanche, Diphelypaea, Orobanche and Phelipanche, native to Turkey, were studied using light and scanning electron microscopy. In this study, 100 accessions belonging to 39 species were investigated. The examined fruits had loculicidal capsules, generally dehiscing with 2 slits, and the seeds were small and with reticulate ornamentation. The basic shape of the seeds in most of the studied taxa was oblong, ellipsoid to ovoid, globose or subglobose. The results indicate that characters such as seed size, shape and color are useless for identification of the taxa at the species level. However, the anticlinal wall pattern and periclinal wall ornamentation proved useful for identifying the different genera. Four morphological types could be distinguished: smooth, perforate, microfibrillar and granulate. Type I corresponds to the genus Cistanche and Orobanche anatolica, whereas types II, III and IV were found in Diphelypaea, Orobanche and Phelipanche, respectively. The utility of seed characteristics is discussed in terms of inter- and intra-generic taxonomy.