In most allopolyploid plants, only homogenetic chromosome pairing occurs in meiosis, as a result of the recognition of genome differentiation by the genetic system regulating meiotic chromosome pairing. The nature of differentiation between chromosomes of closely related genomes is examined here by investigating recombination between wheat chromosome 1A and the closely related homoeologous chromosome lAm of Triticum monococcum. The recognition of the differentiation between these chromosomes by the Phi locus, which prevents heterogenetic chromosome pairing in wheat, is also investigated. Chromosomes lA and lAm are shown to be colinear, and it is concluded that they are differentiated "substructurally." This substructural differentiation is argued to be recognized by the Phi locus. In the absence of Phi, the distribution and frequencies of crossing over between the 1A and lAm homoeologues were similar to the distribution and frequencies of crossing over between IA homologues. The cytogenetic and evolutionary significance of these findings is discussed.Although polyploid plant species contain two or more related pairs of genomes, their meiosis is usually diploid-like, with almost exclusively homogenetic chromosome pairing. Bread wheat (Triticum aestivum L., 2n = 6x = 42) is a good example of this paradox. Bread wheat originated from hybridization of three diploid species, T. urartu Thum. (A genome) (1-3), an extinct or undiscovered population closely related to T. speltoides (Tausch) Gren. (B genome) (4,5), and T. tauschii (Coss.) Schmalh. (D genome) (6, 7). Although the chromosomes of these species have been subjected to significant differentiation, they are still capable of limited chiasmatic pairing at meta-