Deciding that two network flows are essentially the same is an important problem in intrusion detection or in tracing anonymous connections. A stepping stone or an anonymity network may try to prevent flow correlation by delaying the packets, introducing chaff traffic, or even splitting the flow in several subflows. We introduce a game-theoretic framework for this problem. The framework is used to derive the Nash equilibrium under two different adversary models: the first one, when the adversary is limited to delaying packets, and the second, when the adversary also adds dummy packets and removes packets from the flow. As the optimal decoder is not computationally feasible, we restrict the possible decoder to one that estimates and compensates the attack. Our analysis can be used for understanding the limits of flow correlation based on packet timings under an active attacker.