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Methylmercury (MeHg) can form through the microbial transformation of divalent inorganic mercury (HgII). However, it remains unknown whether the total concentration of HgII is a main controlling factor for this methylation process in paddy soils unaffected by local Hg point sources. Here we study the occurrence and controlling factors for MeHg levels in non-contaminated rice paddy soil in Cambodia using 164 soil and 100 overlying water samples from different provinces in wet and dry seasons. Paddy soils were characterized with respect to particle size classes, nutrients, and biogeochemical parameters expected to influence Hg processes. Total mercury (THg) and MeHg concentrations in the soils were not related to geographical location or sampling season but to soil physical and chemical properties. We observed significant positive relationships between the concentrations of divalent inorganic Hg (HgII) and MeHg, suggesting that the concentration of HgII is the main factor determining the net formation of MeHg in non-contaminated rice paddy soils. The %MeHg of THg was used as a proxy of the potential for MeHg formation and was significantly, and inversely, correlated with the redox conditions of the soils, as approximated by the oxidation state of sulfur. The study elucidates critical factors driving MeHg levels in rice paddy soil, enhances the understanding of the MeHg formation process and provides a refined basis for soil quality regulation regarding Hg. The results suggest that reducing Hg inputs to paddies will be effective to lower MeHg concentrations in the soil, ultimately reducing its presence in rice grains.