The main locus responsible for diploid-like behavior of polyploid wheat in meiosis, Ph1, is located on the long arm of chromosome 5B (5BL). It restricts metaphase I pairing to essentially identical homologues. Introduction of 5BL into outcrossing autotetraploid rye severely reduced multivalent formation and increased the frequency of bivalents and univalents, but the key by which homologues were selected for effective pairing was not clear. We created doubled haploids of autotetraploid rye with the long arm of wheat 5BL, verified their nature by DNA markers, and analyzed metaphase I chromosome pairing. The doubled haploid nature guaranteed the presence of pairs of identical and non-identical homologues in each homologous group. The metaphase I pairing patterns were essentially the same as in plants from open pollination, with frequent bivalents and univalents and rare multivalents. The level of pairing was low and depended on the dosage of 5BL. The pairing levels show that unlike in wheat, in rye the Ph1 locus does not use homologue similarity as the criterion in selection of pairing partners. It is possible that the Ph1 of wheat and the rye chromosome pairing system are mutually exclusive. The minimum level of chromosome differences required for effective pairing in rye may be well above the maximum difference level tolerated by the Ph1 system of wheat. In other words, effective chromosome pairing in rye may be possible between non-identical chromosomes that might not normally pair in the Ph1 wheat background.