For more than 1 million years, independent cavefish populations that are geographically and hydrologically isolated from one another have evolved to include about 29 different populations. Among them, the tiny Mexican tetra, Astyanax mexicanus, which comprises river-dwelling surface fish and multiple independently evolved populations of blind cavefish. Many of the behaviors between these cavefish populations differ, suggesting widespread differences in brain structure and function. Although trait evolution in cavefish has been studied for more than a century, little is known about how their brains differ. Moreover, the differences in brain activity have never been explored.