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We present a framework that incorporates the principle of bounded rationality into dynamic stochastic pursuit-evasion games. The solution of a stochastic game is generally characterized by its (Nash) equilibria in feedback form, whose calculation may require extensive computational resources. In this paper, the agents are modeled as bounded rational entities with limited computational capabilities. We illustrate the proposed framework by applying it to a pursuit-evasion game between two aerial vehicles in a stochastic wind field. We show how such a game may be discretized and properly analyzed by casting it as an iterative sequence of finite-state Markov Decision Processes (MDPs). Leveraging tools and algorithms from the cognitive hierarchy theory (“level-k thinking”) we compute the solution of the ensuing discrete game, while taking into consideration the rationality level of each agent. We also present an online algorithm for each agent to infer its opponent's rationality level.