Brachypodium sylvaticumandBrachypodium distachyonwere recently proposed as new model plants because of their small genomes and their phylogenetic position between rice and Triticeae crops. We sequenced a 371-kb region inB. sylvaticum, the largest genomic sequence available so far from this species, providing quantitative data on gene conservation, collinearity and phylogeny. We compared it with orthologous regions from rice and wheat.Brachypodiumand wheat show perfect macro-collinearity of genetic markers, whereas rice contains an approximately 220-kb inversion. Rice contains almost twice as many genes asBrachypodiumin the region studied, whereas wheat has about 40% more. Through comparative annotation, we identified alternative transcripts and improved the annotation for several rice genes, indicating that approximately 15% of rice genes might require re-annotation. Surprisingly, our data suggest that 10–15% of functional sequences in small grass genomes may not encode any proteins. From available genomic and expressed sequence tag sequences, we estimatedBrachypodiumto have diverged from wheat about 35–40 Mya, significantly more recently than the divergence of rice and wheat. However, our data also indicate that orthologous regions fromBrachypodiumand wheat differ considerably in gene content, thus theBrachypodiumgenome sequence probably cannot replace genomic studies in the large Triticeae genomes.