Methods, systems, and computer readable media for heuristics-based adaptive protocol parsing are disclosed. According to one aspect, a method for heuristics-based adaptive protocol parsing includes receiving a message of a first protocol, where the first protocol defines a plurality of valid message formats, and parsing the received message using a protocol tree for determining whether the received message is in one of the plurality of valid message formats. While parsing the received message, heuristics are used to optimize the protocol tree. In one embodiment, the protocol tree is optimized for parsing messages having the message format of a received message.