Pyrite (cubic FeS2) is the most abundant metal sulfide in nature and also the main host mineral of toxic mercury (Hg). Release of mercury in acid mine drainage resulting from the oxidative dissolution of pyrite in coal and ore and rock resulting from mining, processing, waste management, reclamation, and large construction activities is an ongoing environmental challenge. The fate of mercury depends on its chemical forms at the point source, which in turn depends on how it occurs in pyrite. Here, we show that pyrite in coal, sedimentary rocks, and hydrothermal ore deposits can host varying structural forms of Hg which can be identified with high energy-resolution XANES (HR-XANES) spectroscopy. Nominally divalent Hg is incorporated at the Fe site in pyrite from coal and at a marcasite-type Fe site in pyrite from sedimentary rocks. Distinction of the two Hg bonding environments offers a mean to detect microscopic marcasite inclusions (orthorhombic FeS2) in bulk pyrite. In epigenetic pyrite from Carlin-type Au deposit, up to 55 ± 6 at. % of the total Hg occurs as metacinnabar nanoparticles (β-HgSNP), with the remainder being substitutional at the Fe site. Pyritic mercury from Idrija-type Hg deposit (α-HgS ore) is partly divalent and substitutional and partly reduced into elemental form (liquid). Divalent mercury ions, mercury sulfide nanoparticles, and elemental mercury released by the oxidation of pyrite in acid mine drainage settings would have different environmental pathways. Our results could find important applications for designing control strategies of mercury released to land and water in mine-impacted watersheds.