Fishes are particularly sensitive to the effects of environmental conditions during early development, which can significantly impact adult morphology, performance, and survival. Previous research has highlighted the sensitivity of fishes to the effects of temperature during early development on vertebral number and muscle composition, which are both important determinants of an individual's swimming performance. In this study, we investigated the effect of developmental temperature on vertebral and muscle variation, and the subsequent effect of any variation on burst swimming performance in zebrafish (Danio rerio). Following development at a range of temperatures, all individuals were shifted to and maintained at a common temperature before startle responses were recorded and individuals were analyzed for either vertebral number or muscle composition. Our results indicate that developmental temperature does not significantly affect muscle composition, but can affect an individual's vertebral number, and that individuals with more vertebrae achieved greater displacement and velocities during C-start performance. To determine the ecological importance of this vertebral variation and to identify the potential selective factors behind it, we exposed populations of zebrafish with various vertebral numbers to native predators, needlenose garfish (Xenentodon cancila). We found that only caudal vertebral number was related to survival, and that survivors had the same caudal vertebral number across developmental temperatures. Overall, this work highlights the importance of including variation in musculoskeletal anatomy when investigating what is driving selection in fishes. J. Exp. Zool. 325A:25-40, 2016. © 2015 Wiley Periodicals, Inc.