Bacterial genomes exhibit a large amount of variation in their base composition, which ranges from 13% to 75% GC. The evolution and maintenance of this variation has proved to be an enduring puzzle despite decades of theoretical and empirical work. We present an overview of various aspects of this problem, focusing on results from a diverse set of recent studies that use whole-genome sequencing in combination with bioinformatic, phylogenetic, molecular biological, and experimental evolution approaches. We propose that analysis of within-genome variance in GC content is also important to understand how genome-wide base composition has evolved. We close with a discussion of open questions and fruitful avenues of inquiry that may bring us closer to understanding the evolutionary dynamics of bacterial DNA base composition. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 517–528, 2014. © 2014 Wiley Periodicals, Inc.