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Apple orchard surface soils in Japan are polluted with copper (Cu), lead (Pb), and arsenic (As) due to long-term use of metal-based pesticides. We investigated the effects of heavy metals accumulated in the surface soils in apple orchards on the microbial biomass and the microbial communities. Soil samples were taken from a chestnut orchard (unpolluted control) and five apple orchards with different degrees of heavy metal pollution. Total concentrations of Cu, Pb, and As in soil ranged from 29 to 931 mg/kg, 35 to 771 mg/kg, and 11 to 198 mg/kg, respectively. The amount of microbial biomass carbon expressed on a soil organic carbon basis decreased with increasing concentrations of heavy metals. Thus, the heavy metals that accumulated in apple orchard surface soils had adverse effects on the soil microbial biomass. The analysis of phospholipid fatty acid (PLFA) composition indicated that the microbial community structure had changed because of the pesticide-derived heavy metals in soil. The relative abundance of gram-positive bacterial marker PLFAs increased and that of fungal marker PLFA decreased with increasing concentrations of heavy metals in soil. Denaturing gradient gel electrophoreses targeting the 16S ribosomal RNA gene of bacteria and the 18S ribosomal RNA gene of fungi also showed shifts in the composition of bacterial and fungal communities induced by soil pollution with heavy metals. However, the diversity of microbial communities was not significantly affected by the heavy metal pollution. This was attributable to the adaptation of the microbial communities in apple orchard surface soils to heavy metals derived from previously used pesticides.