Molybdenite occurs as isolated crystals, and foliated masses in granite, rhyolite, or pegmatite. Molybdenite is also found in rocks that have been altered by contact and hydrothermal metamorphism. Much of the commercially produced molybdenite occurs as disseminated crystals in porphyry copper deposits where it is produced as a byproduct mineral. Lesser amounts are produced at mines where molybdenite is the primary product.

Minerals that are often found with molybdenite include quartz, pyrite, chalcopyrite, fluorite, cassiterite, scheelite, and wolframite.

Countries with significant molybdenite production include: Armenia, Canada, Chile, China, Iran, Mexico, Mongolia, Peru, Russia and the United States. The United States is a net exporter of molybdenum.