Methylation is an important biotransformation process that limits the toxicity of arsenic (As) in soil. Here we investigated how geomorphology and paddy management influences As speciation, and the abundance and diversity of the arsM gene responsible for bacterial methylation of arsenic. Soil samples collected from paddy and non-paddy fields of Holocene and Pleistocene regions of Bangladesh were incubated under anaerobic conditions to identify how these treatments affected As speciation in soil solution as well as to investigate the changes in relative arsM copy no and diversity in soil. The Holocene soil had higher concentration of soil solution arsenic species (inorganic arsenic, dimethylarsinic acid (DMA), trimethylarsenic oxide (TMAO), with qPCR showing higher copy numbers of both 16S and arsM in Holocene soil compared to Pleistocene soil. Lower soil Eh may explain the higher arsM copy number in Holocene soil, with arsenic methylation known to be increased under anaerobic conditions. The higher pH in Holocene soil may also explain the increase in 16S copy number, with bacteria known to be less abundant in acidic soils. Further to that amplicon sequencing showed an increased species richness (chao1) and diversity (Simpson) for both 16S and arsM in Holocene compare to Pleistocene soil. PiCrust analysis of the 16S amplicon results showed the presence of arsenic metabolism related genes some of which were increased in Holocene compared to Pleistocene soil. The results showed that presence of As soil chemistry strongly correlates with arsenic transformation and copy number of arsenic metabolizing genes and bacterial as well as arsM gene diversity.