The release of Se from shales is poorly understood because its occurrence, distribution, and speciation in the various components of shale are unknown. To address this gap we combined bulk characterization, sequential extractions, and spatially resolved μ-focus spectroscopic analyses and investigated the occurrence and distribution of Se and other associated elements (Fe, As, Cr, Ni, and Zn) and determined the Se speciation at the μ-scale in typical, low bulk Se containing shales. Our results revealed Se primarily correlated with the pyrite fraction with exact Se speciation highly dependent on pyrite morphology. In euhedral pyrites, we found Se(-II) substitutes for S in the mineral structure.However, we also demonstrate that Se is associated with framboidal pyrite grains as a discrete, independent FeSe x phase. The presence of this FeSe x species has major implications for Se release, because FeSe x species oxidize much faster than Se substituted in the euhedral pyrite lattice. Thus, such an FeSe x species will enhance and control the dynamics of Se weathering and release into the aqueous environment.