Protocol reverse engineering (PRE) is essential for understanding undocumented or proprietary communication formats, enabling security-critical tasks such as vulnerability discovery, malware C2 analysis, and IDS signature generation. However, existing PRE techniques rely on brittle hand-written rules, under-model contextual dependencies among neighboring fields, and often fail on messages with nested sub-protocols. We present SEMPRE, a fully automated PRE framework that replaces ad-hoc heuristics with recursive LLM reasoning grounded in fine-grained dynamic program analysis. SEMPRE uses taint-flow and loop traces to guide an LLM-driven tree-of-thought search that slices messages into fields while detecting nested sub-payloads, producing a hierarchical layout. It then infers each field's type and role and iteratively refines boundaries by freezing high-confidence segments and re-running detection under semantic constraints, yielding an EM-style procedure that monotonically improves structure and semantics until convergence. Evaluated on a broad corpus of mainstream protocols against six state-of-the-art (vs. <0.4 for all baselines) and 0.72 for semantic inference (vs. 0.13 for BinPRE). Ablations confirm the contribution of each component, and a case study on a prolific real-world botnet demonstrates practical utility.

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