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Chalcogen vacancies in the semiconducting monolayer transition-metal dichalcogenides (TMDs) have frequently been invoked to explain a wide range of phenomena, including both unintentional p-type and n-type conductivity, as well as sub-band gap defect levels measured via tunneling or optical spectroscopy. These conflicting interpretations of the deep versus shallow nature of the chalcogen vacancies are due in part to shortcomings in prior first-principles calculations of defects in the semiconducting two-dimensional TMDs that have been used to explain experimental observations. Here we report results of hybrid density functional calculations for the chalcogen vacancy in a series of monolayer TMDs, correctly referencing the thermodynamic charge transition levels to the fundamental band gap (as opposed to the optical band gap). We find that the chalcogen vacancies are deep acceptors and cannot lead to n-type or p-type conductivity. Both the (0/−1) and (−1/−2) transition levels occur in the gap, leading to paramagnetic charge states$S=1/2$andS = 1, respectively, in a collinear-spin representation. We discuss trends in terms of the band alignments between the TMDs, which can serve as a guide to future experimental studies of vacancy behavior.