The distribution and speciation of mercury (Hg) were investigated in contaminated soils collected from two adjacent land use systems (arid land and rice paddy) near the Wanshan Mercury mine, SW China. In both sites, fine soil aggregate size fractions (< 231 μm) showed higher total Hg concentrations and higher soil organic matter contents than in larger aggregate size fractions (231 to 2000 μm). Compared to arid land, paddy soils are characterized by higher proportions of fine soil aggregates, higher soil organic matter and higher total Hg content. Soil Hg speciation, based on X-ray absorption spectroscopy (XANES) analysis, indicated that the majority (64–81%) of Hg in soils under both land use systems was associated with metacinnabar (β-HgS), indicating the precipitation of β-HgS in soils. We also observed the presence of bioavailable HgCl2 and Hg(0) in soils at both sites, which may represent a considerable environmental concern. Our study clearly showed that different cultivation practices can largely change the distribution and speciation of Hg in agriculture soils.