Selenium is an essential trace element for humans, animals, and vegetation. Its occurrence in the environment is characterized by specific chemical and biochemical properties that control its elemental solubility, toxicity, and environmental behavior. The Laerma Se-Au deposit and Yutangba Se deposit are two important Se-bearing deposits found recently in China. In one of these areas (Yutangba), a serious environmental impact happened involving Se poisoning. Previous studies have shown that Se in both deposits is closely related to organic matter, especially kerogen fractions, but detailed relationships between Se and kerogen and Se chemical forms were not reported. In this study, the different speciation of Se is identified by transmission electron microscopy (TEM) and other geochemical techniques (infrared spectra (IS) and X-ray diffraction (XRD)) from kerogen samples extracted from ore rocks of both deposits. The occurrence of organically bound Se in the Laerma deposit and elemental Se nanograins in the Yutangba deposit is observed, indicating the diversity of formation mechanisms and possible chemical forms of Se in Se-rich rocks. The formation of elemental Se associated with organic matter is likely related to redox conditions, whereas organic species are related to the higher sulfur content of kerogen and possibly result from S-Se substitutions. This discovery provides new evidence with which to assess potential Se mobility during weathering of ore-bearing rocks. In an altered rock, the elemental Se in kerogen is more steadily mobilized and is potentially accumulated by vegetation, which may explain the sudden prevalence of Se poisoning in the Yutangba area. In contrast, organically bound Se seems more resistant to chemical alteration compared to other Se species so that its bioavailability may be very restricted.