Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although certain anaerobic microorganisms are known to convert inorganic mercury (Hg) to MeHg and the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of microorganisms, the prevalence and diversity of Hg methylators in microbial communities of rice paddy soils remain unclear. Here, we report the abundance and distribution of hgcAB genes using a combination of 3rd-generation PacBio sequencing, metagenomic and quantitative PCR analyses in several mine-impacted paddy soils from southwest China. We show that Hg methylating communities are diverse, with iron-reducing bacteria (i.e., Geobacter) and methanogens as the dominant taxa likely involved in Hg methylation in the soil. Phylogenetic analysis also uncovered some hgcAB sequences closely related to three novel Hg methylators, Geobacter anodireducens, Desulfuromonas sp. DDH964, and Desulfovibrio sp. J2 in these paddy soils. These findings shed new light on microbial community composition and major clades driving Hg methylation in rice paddy soils and have important implications in developing strategies for minimizing bioaccumulation of MeHg in rice grains and thus human exposure.