Comparative genomics is a powerful tool to decipher gene and genome evolution. In this study, a large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for comparative genomic study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Comparative sequence analysis revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 million years ago (mya), differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Large and apparently non-coding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frameshifting insertions/deletions or nonsense mutations.