Maintaining and recovering species diversity is one of the main management goals of forest managers. It is thus important to understand the mechanisms that drive species diversity. The mechanism is strongly related to the harsh biological environment surrounding the tree, especially its interaction with natural enemies, and a well-known mechanism is the Janzen-Connell hypothesis. The hypothesis is best understood by evaluating not only conspecific negative distance-dependent (CNDD) seedling mortality but also replacement of conspecific seedlings by heterospecifics. However, it remains unclear how antagonistic pathogens and mutualistic mycorrhizae affect the strength of replacement. A reciprocal seed-sowing experiment was conducted for five tree species with different mycorrhizal types in forest understorey (FU) and gaps (Gap) in a temperate forest. We investigated seedling mass, mortality, mortality agents, and root infection with arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. In both FU and Gap sites, two AM species were attacked by pathogens causing damping-off and leaf diseases more severely beneath conspecific than heterospecific adults, and more severely among conspecifics than heterospecifics of focal adults, resulting in strong CNDD and replacement, whereas seedling mortality in two EM species due to damping-off pathogens and leaf diseases did not differ among treatments, resulting in weak CNDD and replacement. One AM species showed an intermediate trend between two AM species and two EM species. Thus, CNDD and replacement caused by pathogens were positively correlated in FU but not Gap sites. These traits reveal that replacement closely correlated with CNDD play an important role in maintaining species diversity, especially when gaps are absent. This study also suggest that replacement plays an important role in regulating the spatial distribution of individual trees and subsequent relative abundance of tree species, as well as CNDD effects. Forest managers need to consider differences in the strength of CNDD and replacement between mycorrhizal fungi types when attempting to achieve successful seedling establishment after harvesting without compromising species diversity.