Objective To develop a diagnostic key with third-instar larvae of common flies for habitat investigation and fly larvae identification. Methods A retrieval table was constructed using systematic inductive method and illustrated using dendritic tree. Results The retrieval table included fly larvae of 26 species. All records were divided into two categories according to the existence of posterior process on the 8th abdominal segment. Larvae without posterior process on the 8th abdominal segment were further divided into two categories according to peritreme integrity.Conclusion The retrieval table is simple, intuitive, and easy to use. It can be applied in habitat investigation, monitoring of fly larvae, hygiene assessment, management for epidemic foci of vector-borne diseases, and forensic insect identification.