Conservation ecologists have long argued over the best way of placing reserves across an environment to maximize population diversity. Many have studied the effect of protecting many small regions of an ecosystem vs. a single large region, with varied results. However, this research tends to ignore evolutionary dynamics under the rationale that the spatiotemporal scale required is prohibitive. We used the Avida digital evolution research platform to overcome this barrier and study the response of phenotypic diversity to eight different reserve placement configurations. The capacity for mutation, and therefore evolution, substantially altered the dynamics of diversity in the population. When mutations were allowed, reserve configurations involving a greater number of consequently smaller reserves were substantially more effective at maintaining existing diversity and generating new diversity. However, when mutations were disallowed, reserve configuration had little effect on diversity generation and maintenance. While further research is necessary before translating these results into policy decisions, this study demonstrates the importance of considering evolution when making such decisions and suggests that a larger number of smaller reserves may have evolutionary benefits.