During meiosis, chromosomes are sorted into homologous pairs as a preface to their intimate association via recombination and synapsis. However, little is known about the mechanism used to distinguish homologous chromosomes from other chromosomes present in the nucleus. Studies in wheat (Triticum aestivum) have shown that the Pairing homoeologous 1 (Ph1) locus is required to suppress interactions between genetically similar homoeologous chromosomes. Here we show that absence of Ph1 causes increased transcription of Asynapsis 1 (ASY1), a gene that encodes an axial-element-associated protein that is essential for synapsis and cross-over formation in Arabidopsis and rice. Localisation of ASY1 during meiosis is also affected by deletion of Ph1. In addition, transgenic wheat mutants with decreased activity of TaASY1 display reduced synapsis during prophase I and exhibit pairing between homoeologous chromosomes at metaphase I. These results suggest that ASY1 is required to promote interactions between homologous chromosomes in bread wheat, and that Ph1 has a gene regulatory role, which is consistent with its suggested genetic identity as a Cdk-like gene. Broader implications of this research suggest that we could use the Taasy1 mutants to assess their efficacy in alien chromatin introgression studies, as seen with the ph1b mutant.