Nanoparticulate mercury (Hg-NPs) are ubiquitous in nature. However, the lack of data on their concentration in soils impedes reliable risk assessments. This is due to the analytical difficulties resulting from low ambient Hg concentrations and background interferences of heterogeneous soil components. Here, coupled to single particle inductively coupled plasma-mass spectrometry (spICP-MS), a standardized protocol was developed for extraction and quantification of Hg-NPs in natural soils with a wide range of properties. High particle number-, particle mass-, and total mass-based recoveries were obtained for spiked HgS-NPs (74−120%). Indigenous Hg-NPs across soils were within 107 −1011 NPs g−1 , corresponding to 3−40% of total Hg on a mass basis. Metacinnabar was the primary Hg species in extracted samples from the Wanshan mercury mining site, as characterized by X-ray absorption spectroscopy and transmission electron microscopy. In agreement with the spICP-MS analysis, electron microscopy revealed comparable size distribution for nanoparticles larger than 27 nm. These indigenous Hg-NPs contributed to 5−65% of the measured methylmercury in soils. This work paves the way for experimental determinations of indigenous Hg-NPs in natural soils, which is critical to understand the biogeochemical cycling of mercury and thereby the methylation processes governing the public exposure to methylmercury.