Wheat is one of the most important world’s crop species, however genomic studies are made difficult by the high complexity and width of its genome, which is very large and polyploid. For these reasons, sequence information from sequenced genomes of model species together with the study of the syntenic relationships among them represent a very important tool to elucidate the structure and the function of the complex wheat genome. In the present work, we analyzed the syntenic relationship existing between wheat, rice and Brachypodium distachyon, focusing in particular on SNP markers previously mapped on wheat 5A chromosome. The comparative genomic study described in the present work confirmed the great importance of sequence information associated with SNP markers combined with comparative genomics studies. In particular, the work evidenced a co-linearity and a good conservation of loci order between wheat and the two model reference species; such studies will be very useful for understanding the evolution of grass genomes, map based cloning of important genes, and for future wheat genome sequencing and the acceleration of genomic based improvement of these important crops.