Genome structure exhibits remarkable plasticity within Zea mays. To examine how haplotype structure has evolved within the Andropogoneae tribe, we have analyzed the bz gene-rich region of maize, the Zea teosintes mays ssp. mexicana, luxurians and diploperennis, Tripsacum dactyloides, Coix lacryma-jobi, and Sorghum propinquum. We sequenced and annotated BAC clones from these species and reannotated the orthologous Sorghum bicolor region. Gene colinearity in the region is well conserved within the genus Zea. However, the orthologous regions of Coix and Sorghum exhibited several micro-rearrangements relative to Zea, including addition, truncation, and deletion of genes. The stc1 gene, involved in the production of a terpenoid insect defense signal, is evolving particularly fast and its progressive disappearance from some species is occurring by microhomology-mediated recombination. LTR retrotransposons are the main contributors to the dynamic evolution of the bz region. Common transposon insertion sites occur among haplotypes from different Zea mays subspecies, but not outside of the species. As in Zea, different patterns of interspersion between genes and retrotransposons are observed in Sorghum. We estimate that the average divergence times between maize and Tripsacum, Coix and Sorghum are 8.5, 12.1, and 12.4 million years ago (MYA), respectively, and that between Coix and Sorghum is 9.3 MYA. A comparison of the bz orthologous regions of Zea, Sorghum, and Coix with those of Brachypodium, Setaria, and Oryza allows us to infer how the region has evolved by the addition and deletion of genes in the approximately 50 MY since these genera diverged from a common progenitor.