Arsenic (As) is a toxic metalloid that occurs naturally and is widely distributed in the environment. The inorganic compounds arsenite (As(III)) and arsenate (As(V)) are the most prevalent As species in the biosphere, the former being predominant in reducing environments. Some microbes can methylate As(III) to produce methylated As compounds. This biotransformation alters the fate and toxicity of As, and is a key component of its biogeochemical cycle. Arsenic methylation is often observed in rice paddy fields, where it is enhanced upon soil flooding (i.e., under anoxic conditions). The methylated products can be absorbed by the rice plant through the roots and accumulate in the grains, and can also induce the sterility of the plant. This microbial transformation may thus pose a threat to both food security and safety. However, very few anaerobic As-methylating microbes have been isolated, which precludes further understanding of the controls on this transformation and its biological function. Their isolation is laborious because traditional techniques for the isolation of environmental anaerobes are time-consuming, and the As-methylating phenotype cannot be easily screened. To tackle these challenges, we developed an alternative isolation approach which consists of trapping and growing individual soil microbes within permeable compartments (hydrogel capsules), and subsequent sorting using fluorescence-activated cell sorting (FACS) to distribute compartmentalized isolates in microwell plates for further growth. This approach enabled the cultivation of anaerobic taxa which fail to grow on agar-based medium. Further, we employed a bacterial biosensor that fluorescently responds to methylated As to functionally screen for the isolates showing methylation capacity. This approach allowed us to rapidly isolate anaerobic As-methylating strains from a paddy soil.