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The neurotoxin methylmercury (MeHg) is produced mainly from the transformation of inorganic Hg by microorganisms carrying the hgcAB gene pair. Paddy soils are known to harbor diverse microbial communities exhibiting varying abilities in methylating inorganic Hg, but their distribution and environmental drivers remain unknown at a large spatial scale. Using hgcA gene amplicon sequencing, this study examined Hg-methylating communities from major rice-producing paddy soils across a transect of ∼3600 km and an altitude of ∼1300 m in China. Results showed that hgcA⁺ OTU richness was higher in tropical and subtropical paddy soils compared to temperate zones. Geobacteraceae, Smithellaceae, and Methanoregulaceae were identified as the dominant hgcA⁺ families associated with MeHg production, collectively accounting for up to 77% of total hgcA⁺ sequences. Hierarchical partitioning analyses revealed that pH was the main driver of hgcA genes from Geobacteraceae (14.8%) and Methanoregulaceae (16.3%), while altitude accounted for 21.4% of hgcA genes from Smithellaceae. Based on these environmental preferences, a machine-learning algorithm was used to predict the spatial distribution of these dominant hgcA⁺ families, thereby providing novel insights into important microbial determinants for improved prediction of MeHg production in paddy soils across China.