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The existence of distinct species of life is generally explained by the genetic process of reproduction without recombination between populations and/or the ecological process of adaptation to different environments. Both processes affect prokaryotes, and have shaped existing genomes. Here, we use comparative genomic techniques to evaluate the dynamics of divergence among species of the Enterobacteriaceae. Bacteria such as Escherichia coli preferentially acquire allelic variants from closely related organisms (i.e. other E. coli) rather than from more diverged bacteria. Ecological differences between donor and recipient affect the probability of allelic variants becoming fixed across the recombining population. We examine the history of recombination among groups of genomes that no longer recombine with each other, but retain sufficient conservation of ancestral nucleotide sequences to allow recombination to be inferred. From these analyses, we conclude that substantial levels of recombination occurred between E. coli and diverging lineages even after some regions of the genomes had acquired many nucleotide differences. We identify two evolutionary radiations leading to E. coli where the disparity among loci confounds the phylogenetic relationships among species, as evidenced by topological incongruence among gene trees. The forces affecting recombination, reflected in both pairwise divergence and topologically informative sites, vary across regions of the genome measuring tens of kilobases. To examine the relationship between ecological differentiation and genetic recombination, we characterize differences that could be responsible for ecological differentiation among these species. Some of the loci with the most apparent functional differences (i.e. the gain and loss of genes) are associated with the greatest levels of sequence divergence between species, consistent with the hypothesis that ecological divergence interferes with homologous recombination, and therefore drives sequence divergence and genetic isolation. To investigate the role of more subtle ecological differentiation, we develop a statistical framework to evaluate codon usage bias of each protein-coding gene, taking into account the stochastic balance between codon selection, which is driven by the need for high expression, and mutational biases. This tool will be useful in future studies examining codon selection as contribution to diversification among the ecologically diverse species of Enterobacteriaceae.