The ATLAS experiment at LHC is carrying on a wide programme to study the production properties of conventional and exotic quarkonium, beauty, and charm bound states. The latest results on J/$\psi$, $\psi$(2s) and X(3872) production at 7, 8, and 13 TeV, together with D meson production with Run-1 are presented. Studies of associated production of charmonium with vector bosons, searches for exotic states in the bottomonium sector and a new measurement of the ratio of b-quark fragmentation functions are also briefly presented.
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