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Abstract Optically active point defects in wide‐bandgap semiconductors have been demonstrated to be attractive for a variety of quantum and nanoscale applications. In particular, color centers in hexagonal boron nitride (hBN) have recently gained substantial attention owing to their spectral tunability, brightness, stability, and room‐temperature operation. Despite all of the recent studies, precise detection of the defect‐induced mid‐gap electronic states (MESs) and their simultaneous correlations with the observed emission in hBN remain elusive. Directly probing these MESs provides a powerful approach toward atomic identification and optical control of the defect centers underlying the sub‐bandgap emission in hBN. Combining optical and electron spectroscopy, the existence of mid‐gap absorptive features is revealed at the emissive sites in hBN, along with an atom‐by‐atom identification of the underlying defect configuration. The atomically resolved defect structure, primarily constituted by vacancies and carbon/oxygen substitutions, is further studied via first‐principles calculations, which support the correlation with the observed MESs through the electronic density of states. This work provides a direct relationship between the observed visible emission in hBN, the underlying defect structure, and its absorptive MESs, opening venues for atomic‐scale and optical control in hBN for quantum technology.