In order to study the phylogeny of Aegilops mutica in the genera of Triticum and Aegilops, variations in chloroplast and mitochondrial DNA regions were investigated by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis. Nine lines, each of Ae. mutica and Ae. speltoides, were studied together with nine other Triticum and Aegilops species, including T. aestivum. By analyzing 9.7-kb chloroplast and 13.1-kb mitochondrial DNA regions, a total of 268 bands were detected, of which 176 (65.7%) showed variation within and/or between species. The level of intraspecific variation of Ae. mutica was lower than that of Ae. speltoides. The low level of the intraspecific variation of Ae. mutica was contrary to the expectation from previous studies on morphological and cytolo-gical characters. In the phylogenetic trees based on SSCP, Ae. mutica, Ae. speltoides and the other four species of the section Sitopsis (the subsection Emarginata) were separated into three different clusters. In addition, T. aestivum was included in the cluster of Ae. speltoides in the phylogenetic trees. This result suggests that Ae. speltoides is the cytoplasmic donor of common wheat.