Experimental microbial evolution (EME) and its variant, adaptive laboratory evolution (ALE), are emerging empirical strategies for understanding fundamental biological processes in microbes. Integration of high throughput analytical methods combined with genetic selection leverage the power of these methods, particularly ALE, for the production of new biological traits while providing insight into their mechanistic basis. Though traditionally applied to model organisms, in this chapter, these methods are extended to studies using microbial extremophiles with an emphasis on current studies from our laboratory because of the near absence of published literature. Theoretic considerations are presented first. These are followed by descriptions of technologies that are required to extend these evolutionary methods to the study of extremophiles. Finally, the application of ALE is demonstrated using two distinct types of extremophiles. These include the hyperthermophilic anaerobic bacterium Thermotoga maritima, and the extremely thermoacidophilic archaeon Sulfolobus solfataricus. For T. maritima, the evolutionary genomics of deletion formation is presented, and for S. solfataricus, the role of insertion sequence elements is considered during the evolution of increased thermoacidophily. These examples demonstrate the utility of experimental evolutionary methods in association with extremophiles.