Molybdenite is a common sulfide hosting many trace elements. Trace elements in molybdenite from individual deposits have been widely used to constrain the source and conditions of ore-forming fluids. However, the relationship between the trace element composition of molybdenite and deposit types has not been well investigated from a large dataset. Here, simple statistics and partial least squares-discriminant analysis (PLS-DA) were used to determine whether different types of deposits can be distinguished by trace elements in molybdenite and what factors control the variations in trace element composition based on published laser ablation ICP-MS data. Molybdenite from porphyry deposits is separated from that from quartz veins, greisen Sn-W, granite vein Mo, and granodiorite Mo deposits. The former is characterized by relatively high Re, Cu, Ag, Se, Pb, Bi, and Te contents, whereas the latter has higher Ni, Co, Sn, Sb and W contents. Molybdenite from the quartz vein Au +/- W deposits (Au-dominated), and porphyry Cu-Au-Mo (moderate Au) are separated from other deposits without gold due to positive correlations with Au, Sb, Te, Pb, and Bi for the former. Assemblages of Au-Sb-Te-Pb-Bi in molybdenite are thus useful to discriminate as to whether deposits contain gold and the degree of gold mineralization. Higher oxygen fugacity is responsible for the relative enrichment of W in molybdenite from greisen Sn-W deposits, whereas lower oxygen fugacity results in the relative enrichment of Re in molybdenite from porphyry Cu +/- Mo +/- Au and Mo +/- Cu +/- Au deposits. There are some limitations to using molybdenite as an indicator mineral because of the complex occurrences of elements in molybdenite, large compositional variations within a specific deposit type, and an imbalanced dataset. To develop molybdenite as an indicator mineral tool, further work should be carried out to overcome these limitations. This study provides an attempt to classify deposit types using molybdenite trace elements and has important implications for ore genesis research and mineral exploration.