Aegilops triuncialis is an amphidiploid between Ae. umbellulata and Ae. caudata. RFLP (restriction fragment length polymorphism) analysis of the chloroplast DNAs in a world collection of this species distinguished 3 types of accessions; one with chloroplast DNA similar to that of Ae. umbellulata, the second with DNA similar to that of Ae. caudata, and the third differing distinctly from the first two. This third type of chloroplast DNA was present only in the Baku (Azerbaijan) population of Ae. triuncialis. Our investigation, which used plasmon analysis followed by genome and morphological analyses, led to the conclusion that accessions of this population should be reallocated to Ae. kotschyi, for the following reasons: (1) Transfer of the plasmon of a third type accession, No. 2972, to 12 common wheat genotypes showed that this plasmon’s effects on various wheat characters differ markedly from those of the Ae. umbellulata and Ae. caudata plasmons but are similar to those of the Ae. kotschyi and Ae. variabilis plasmons. (2) Reinvestigation of RFLP data on organellar DNAs reported previously supports the above findings. (3) Observations of meiotic chromosome pairing, and the pollen and seed fertilities of the F₁ hybrids between Accession 2927 and a few standard accessions of Ae. triuncialis, Ae. kotschyi, and Ae. variabilis showed that the genome of Accession 2927 is homologous to the genomes of the last 2 species. Moreover, (4) morphological studies indicated that all 5 accessions of the Baku population belong to Ae. kotschyi, not to Ae. triuncialis. Our present investigations show that plasmon analysis provides critical information for the correct classification of a plant taxon whose taxonomic allocation is problematical. In addition, our findings show that the Ae. kotschyi collection at Kyoto University formerly thought to be missing samples from Transcaucasia, covers the entire distribution area.