There is a need for a better public understanding of evolutionary relatedness including its relevance to socio-scientific issues such as conservation and health. As venues that play an important role in communicating about evolution, natural history museums have an opportunity to explore novel means of enhancing visitor learning in this area. We describe the design, testing, modification, and evaluation of an immersive, problem-solving educational game on the topic of evolution using specimens on display in a natural history museum. Natural History Mystery invites small teams of players to solve a series of puzzles to identify the source of a zoonotic disease. In the process, they use existing exhibits and supporting game components to learn about shared characters, common ancestry, and relatedness. The game was iteratively designed through multiple rounds of trial testing with families and other groups. A summative assessment performed by an external evaluator concluded that, through the game, players had fun, explored the museum in new ways, and felt they learned and developed new skills. The evaluation found that participants learned about evolutionary relationships and made connections between evolution and medical applications. We share details about game/puzzle design and development along with lessons learned, providing a model for other institutions to create their own themed puzzle-hunt game customized to their site.