Plants are the essential factors shaping soil microbial community (SMC) structure. Whenmost studies focus on the difference in the SMC structure associated different plantspecies, the variation in the SMC structure associated with phylogenetically close speciesis less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally importantplant groups; however, their inflfluences on the SMC structure are seldom compared, andthe variation in the SMC structure among legume or grass species is largely unknown.In this study, we grew three legume species vs. three grass species in mesocosms, andmonitored the soil chemical property, quantifified the abundance of bacteria and fungi. TheSMC structure was also characterized using PCR-DGGE and Miseq sequencing. Resultsshowed that legume and grass differentially affected soil pH, dissolved organic C, totalN content, and available P content, and that legume enriched fungi more greatly thangrass. Both DGGE profifiling and Miseq-sequencing indicated that the bacterial diversityassociated with legume was higher than that associated with grass. When legumeincreased the abundance of Verrucomicrobia, grass decreased it, and furthermore,linear discriminant analysis identifified some group-specifific microbial taxa as potentialbiomarkers of legume or grass. These data suggest that legume and grass differentiallyselect for the SMC. More importantly, clustering analysis based on both DGGE profifilingand Miseq-sequencing demonstrated that the variation in the SMC structure associatedwith three legume species was greater than that associated with three grass species.