Purpose <p>Arsenic pollution in soils, especially in metal mining areas and paddy fields, has garnered significant attention. Moreover, microorganisms play crucial roles in modifying arsenic mobility, speciation, and toxicity through the evolution of various arsenic metabolism genes (AMGs). However, investigations into the potential influencing factors of arsenic pollution and AMGs at the national scale remain limited. Therefore, in this study, arsenic and its associated metabolism genes were comprehensively investigated in mine and paddy soils across China, providing new insights into the drivers of arsenic pollution and microbial arsenic metabolism in soils.</p> Methods <p>The species sensitivity distribution and the joint probability curve were integrated to assess the probabilistic ecological risk of arsenic. Furthermore, meta-analysis and the Geodetector model were utilized to explore the relationships between arsenic pollution and potential influencing factors. Additionally, metagenomic analysis was employed to investigate the abundance, diversity, taxonomic composition, and influencing factors of AMGs.</p> Results <p>Our results indicate a significantly greater ecological risk of arsenic in mine soils than in paddy soils. The soil type, mean annual temperature (MAT), and total sulfur (TS) significantly influenced the soil arsenic pollution level. Diverse and abundant AMGs were detected in both mine and paddy soils. The high abundance of the <i>arsR</i> gene, which encodes a transcriptional repressor protein regulating the arsenic resistance (<i>ars</i>) operon, and the <i>arsC</i> gene, which encodes cytoplasmic arsenate reductase, along with their co-occurrence in almost all of the identified metagenome-assembled genomes (MAGs), further emphasized their pivotal contribution to soil arsenic metabolism. The diversity of AMGs in mine soils was significantly greater than that in paddy soils. The microorganisms hosting AMGs were classified into bacteria (78.1%), archaea (20.7%), and fungi (1.2%). The mean annual precipitation (MAP) and soil pH were identified as crucial influencing factors for the abundance of AMGs in both mine and paddy soils.</p> Conclusion <p>This study enhances our understanding of arsenic and AMGs in soils, thereby establishing a theoretical basis for effective management and mitigation strategies against arsenic pollution.</p>