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Photonic sensors that are able to detect and track biochemical molecules offer powerful tools for information acquisition in applications ranging from environmental analysis to medical diagnosis. The ultimate aim of biochemical sensing is to achieve both quantitative sensitivity and selectivity. As atomically thick films with remarkable optoelectronic tunability, graphene and its derived materials have shown unique potential as a chemically tunable platform for sensing, thus enabling significant performance enhancement, versatile functionalization and flexible device integration. Here, we demonstrate a partially reduced graphene oxide (prGO) inner-coated and fiber-calibrated Fabry-Perot dye resonator for biochemical detection. Versatile functionalization in the prGO film enables the intracavity fluorescent resonance energy transfer (FRET) to be chemically selective in the visible band. Moreover, by measuring the intermode interference via noise canceled beat notes and locked-in heterodyne detection with Hz-level precision, we achieved individual molecule sensitivity for dopamine, nicotine and single-strand DNA detection. This work combines atomic-layer nanoscience and high-resolution optoelectronics, providing a way toward high-performance biochemical sensors and systems.