Genome research on oat (Avena sativa L.) has received less attention than wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) because it is a less prominent component of the human food system. To assess the potential of the model grass Brachypodium distachyon (L) P. Beauv. as a surrogate for oat genome research, the whole genome sequence (WGS) of B. distachyon was employed for comparative analysis with oat genetic linkage maps. Sequences of mapped molecular markers from one diploid Avena spp. and two hexaploid oat maps were aligned to the B. distachyon WGS to infer syntenic relationships. Diploid Avena and B. distachyon exhibit a high degree of synteny with 18 syntenic blocks covering 87% of the oat genome, which permitted postulation of an ancestral Avena spp. chromosome structure. Synteny between oat and B. distachyon was also prevalent, with 50 syntenic blocks covering 76.6% of the ‘Kanota’ × ‘Ogle’ linkage map. Coalignment of diploid and hexaploid maps to B. distachyon helped resolve homeologous relationships between different oat linkage groups but also revealed many major rearrangements in oat subgenomes. Extending the analysis to a second oat linkage map (Ogle × ‘TAM O‐301’) allowed identification of several putative homologous linkage groups across the two oat populations. These results indicate that the B. distachyon genome sequence will be a useful resource to assist genetics and genomics research in oat. The analytical strategy employed here should be applicable for genome research in other temperate grass crops with modest amounts of genomic data.