Begonia is one of the ten largest angiosperm genera with over 1,500 species found throughout the tropics. To use this group as a model for the evolution of diversity in tropical herbaceous plants, we have produced three species transcriptomes, physical genome size measures, and two backcross genetic maps. We chose to focus on two Central American species, B. conchifolia and B. plebeja, and one SE Asian species, B. venusta, allowing us to pose questions at widely different evolutionary scales within the genus. We used next generation sequencing of cDNA libraries to produce annotated transcriptome databases for each of the three species. Though Begonia is functionally diploid, transcriptome analysis suggested a genome duplication occurred at or near the base of the Begonia clade. The genetic maps were built from first generation backcrosses in both directions between B. plebeja and B. conchifolia using 105 SNP markers in genes known to regulate development that were identified from the transcriptomes and the map bulked out with 226 AFLP loci. The genetic maps had 14 distinct linkage groups each and mean marker densities of between 3.6 and 5.8 cM providing between 96 and 99 % genomic coverage within 10 cM. We measured genome size 1C value of 0.60 and 0.63 pg for B. conchifolia and B. plebeja corresponding to recombination rates of between 441 and 451 Kb per cM in the genetic maps. Altogether, these new data represent a powerful new set of molecular genetic tools for evolutionary study in the genus Begonia.