Triticum peregrinum Hackel (syn. Aegilops variabilis Eig) and T. kotschyi (Boiss.) Bowden (syn. Ae. kotschyi Boiss.) are closely related allotetraploid species. Previous research indicated that they have a pair of U genomes from diploid T. umbellulatum (Zhuk.) Hackel and a pair of S genomes from a diploid species of Triticum section Sitopsis. To reinvestigate the origin of their genomes, we identified diagnostic bands in Southern blots hybridized with 27 cloned repeated nucleotide sequences and one 5S rRNA gene clone for all diploid species of Triticum L. sensu Bowden. The presence of each diagnostic band was then determined in the two tetraploid species. One pair of the genomes in both tetraploid species was found to be virtually identical to the U genome of T. umbellulatum and the other to the S1 genome of T. longissimum (Schweif. et Muschl.) Bowden or T. sharonense (Eig) Waines &Johnson (syn. Aegilops sharonensis Eig) or the internode in the phylogenetic tree of Triticum immediately preceding the divergence of T. longissimum and T. sharonense. The source of the S genomes in T. kotschyi and T. peregrinum inferred from our data differs from that inferred from cpDNA. This indicates the need to investigate the origin of nuclear genomes with nuclear genetic markers. No evidence for an extensive modification of the S genome relative to that of T. longissimum or T. sharonense was found in either tetraploid.Key words: phylogeny, polyploids, Triticum, Aegilops, Aegilops kotschyi, Aegilops variabilis, genome origin, genome modification.