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Flavor violating processes in the lepton sector have highly suppressed branching ratios in the standard model mainly due to the tiny neutrino mass. This means that observing lepton flavor violation (LFV) in the next round of experiments would constitute a clear indication of physics beyond the standard model (BSM). We revisit a discussion of one possible way to search for LFV, muonium-antimuonium oscillations. This process violates muon lepton number by two units and could be sensitive to the types of BSM physics that are not probed by other types of LFV processes. Using techniques of effective field theory, we calculate the mass and width differences of the mass eigenstates of muonium. We argue that its invisible decays give the parametrically leading contribution to the lifetime difference and put constraints on the scales of new physics probed by effective operators in muonium oscillations.