The first detailed linkage maps of two bermudagrass species, Cynodon dactylon (T89) and C. transvaalensis (T574), provide a foundation for inferring gene arrangements along the chromosomes of a hypothetical common Cynodon ancestor, and in turn aligning the Cynodon genome to those of cereal models. The map of T89 is based on 155 single-dose restriction fragment (SDRF) loci and 17 double-dose restriction fragment (DDRF) loci on 35 linkage groups, with an average marker spacing of 15.3 cM. The map of T574 is based on 77 SDRF loci on 18 linkage groups with an average marker spacing of 16.5 cM. Using these maps we have estimated the recombinational length of the T89 and T574 genomes at 3012 and 1569 cM respectively, which are 61% and 62% covered by our maps. Sixteen T89 linkage groups were arranged into 4 complete homologous sets and 8 into 4 incomplete homologous sets, while 15 T574 linkage groups were arranged into 7 complete homologous sets, all on the basis of multi-locus probes and repulsion linkages. Eleven T89, and three T574 linkage groups remain un-assigned. In each parent, consensus maps were built based on alignments of homologous linkage groups. Four ancestral chromosomes were inferred after aligning T89 and T574 parental consensus maps using multi-locus probes. The inferred ancestral marker orders were used in comparisons to a detailed Sorghum linkage map using 40 common probes, and to the rice genome sequence using 98 significant BLAST hits. We found significant hits to regions of all 12 rice chromosomes, and common probes with regions of all 10 Sorghum linkage groups. A useful level of colinearity across large chromosomal segments indicates the ability to leverage structural and functional information from rice and other cereal models in the study and improvement of Cynodon.