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In this study, mercury (Hg)\u2010methylating microbes with the potential biomarker gene <jats:italic>hgcA<\/jats:italic> were obtained from 45 paddy soil samples in mercury mining areas in Fenghuang, Wanshan, and Xunyang. In different areas, the abundance of the <jats:italic>hgcA<\/jats:italic> gene was affected by different environmental factors, including organic matter, <jats:styled-content style=\"fixed-case\">pH<\/jats:styled-content>, total carbon content, total nitrogen content, and total mercury content. Phylogenetic analysis showed that <jats:italic>hgcA<\/jats:italic> microbes in paddy soils were potentially members of the phyla Proteobacteria, Euryarchaeota, Chloroflexi, and two unnamed groups. Canonical correspondence analysis showed that <jats:styled-content style=\"fixed-case\">pH<\/jats:styled-content> and organic matter impacted the <jats:italic>hgcA<\/jats:italic> gene diversity and the microbial community structures in paddy soils. 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