The composition and structure of the soil microbial community is a key determinant of the growth and development of the prized edible mycorrhizal fungus Tricholoma matsutake and its shiro. However, little is known about any differences in the composition and structure of soil microbial communities between shiro and non-shiro soils, and whether these differences vary among different host forest types. In this study, we used phospholipid fatty acid (PLFA) analysis to compare the soil microbial communities of shiro and non-shiro soils in two forests dominated by Quercus semecarpifolia and Pinus densata in Shangri-La County in northwest Yunnan, China. We found that:1) fungi (18:2ω6,9c, 18:1ω9c, 18:3 w6c (6,9,12)), gram-negative bacteria (19:0 cyclo w8c), gram-positive bacteria (15:0 iso), and non-specific PLFAs (16:0, 17:1 anteiso B, 18:1 w6c, 16:1 w6c, 18:0) were the dominant microbial groups in shiro; 2) the percentage of fungi and the biomass ratio of fungi to bacteria (F/B) were significantly higher in shiro than in non-shiro soils, but the percentages of gram-negative bacteria and gram-positive bacteria, and the evenness (J) of total PLFAs were lower in shiro than in non-shiro soils; 3) soil microbial community structure differed significantly between shiro and non-shiro soils and between the two forest types, and the difference between shiro and non-shiro soils was greater than the difference between the two forest types; 4) there was no interaction between shiro and forest type, which indicates that shiro microbial community characteristics did not differ between host forest types; 5) soil chemical properties differed significantly between the two forest types; however, no obvious difference was found between shiro and non-shiro soils. Our findings revealed differences in the composition and structure of shiro and non-shiro soil microbial communities, and that these differences were consistent across both Quercus semecarpifolia and Pinus densata forests.