Meiotic chromosome pairing data from hybrids of diploid Aegilops [A. squarrosa, A. uniaristata], Haynaldia [H. villosa] and Triticum [T. monococcum, T. aegilopoides] species, previously published by Dr. E.R. Sears, are interpreted to indicate that intraspecific genotypic differences control the amount of homoeologous chromosome pairing in diploid interspecific hybrids. There was immediate diploidization, with continued control of homoeologous pairing, when these hybrids were made into amphidiploids. This suggests that loci analagous to the Ph allele in hexaploid T. aestivum are already present in genotypes of diploid species and do not necessarily have to arise by mutation or translocation after polyploid formation. A genetic model for the control of homoeologous chromosome pairing is presented, and the importance of this control as an isolating mechanism among diploid populations is stressed. The relevance of genes that promote and suppress homoeologous chromosome pairing at meiosis to the technique of genome analysis is discussed, especially as to the restrictions they place on the use of this technique to indicate evolutionary relationships.