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Chalcogen vacancies are generally considered to be the most common point defects in transition metal dichalcogenide (TMD) semiconductors because of their low formation energy in vacuum and their frequent observation in transmission electron microscopy studies. Consequently, unexpected optical, transport, and catalytic properties in 2D-TMDs have been attributed to in-gap states associated with chalcogen vacancies, even in the absence of direct experimental evidence. Here, we combine low-temperature non-contact atomic force microscopy, scanning tunneling microscopy and spectroscopy, and state-of-the-art ab initio density functional theory and GW calculations to determine both the atomic structure and electronic properties of an abundant chalcogen-site point defect common to MoSe and WS monolayers grown by molecular beam epitaxy and chemical vapor deposition, respectively. Surprisingly, we observe no in-gap states. Our results strongly suggest that the common chalcogen defects in the described 2D-TMD semiconductors, measured in vacuum environment after gentle annealing, are oxygen substitutional defects, rather than vacancies., This work was supported by the Center for Computational Study of Excited State Phenomena in Energy Materials (C2SEPEM), which is funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division under Contract No. DE-AC02-05CH11231, as part of the Computational Materials Sciences Program. Work performed at the Molecular Foundry was also supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under the same contract number. S.B. acknowledges fellowship support by the European Union under FP7-PEOPLE-2012-IOF-327581. S.B. and M.M.U acknowledge Spanish MINECO (MAT2017-88377-C2-1-R). S.R.A acknowledges Rothschild and Fulbright fellowships. B.S. appreciates support from the Swiss National Science Foundation under project number P2SKP2_171770. A.P. and O.V.Y. acknowledge support by the ERC Starting grant “TopoMat” (Grant No. 306504). M.F.C. acknowledges support from the U.S. National Science Foundation under project number EFMA-1542741. C.H. acknowledges support from NRF grant funded by the Korea government (MSIT) (No. 2018R1A2B6004538). DFT calculations were performed at the Swiss National Supercomputing Centre (CSCS) under project s832 and the facilities of Scientific IT and Application Support Center of EPFL. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 for the GW calculations. This research used resources of the Advanced Light Source, which is a DOE Office of Science User Facility under contract no. DE-AC02-05CH11231.