The object of this study was to determine the role of species in maintaining local tree diversity and, thereby, identify processes that structure and maintain the community biodiversity of typical, natural, mid-subtropical broad-leaved forests. Two typical forest sample plots located in Wanmulin Reserve, Fujian Province, were investigated. The individual species-area relationship (ISAR) analysis method was used to investigate two scenarios, without or with tree layer stratification. The results show that the tree layers of both plots could be divided into the light receiving layer (LRL) and non-light receiving layer (NLRL). Overestimation of the relative importance of non-random effects could be avoided when specifying trees distributed in the LRL as focal species in ISAR analysis. This implies that the tree diversity of the two studied forest communities is structured by neutral factors because most species in the LRL or tree layer were neutral species of the local tree diversity.