Ectomycorrhizal (EM) symbiosis is a vital mutualistic interaction in natural ecosystems, and the mechanisms of partner selection are complex. Recent studies showed root-associated EMF communities were affected by host identity and geography, but their relative importance varied by sites. EMF preferences of the host differed among geography, affected by environments and availability of EMF resources, however, there is less information about EMF pools (soil). This study investigated EMF communities of bulk soil (background) and root (host selection) of three pine species using Illumina MiSeq sequencing, to understand the host’s EMF range and preference. The results showed that Abies kawakamii and Tsuga chinensis var. formosana (Abietoideae) shared a high-proportion of EMF, and they preferred common EMF with different dominance, whereas Picea morrisonicola (Pinoideae) preferred various EMF which not associated with A. kawakamii and T. chinensis. The core EMF, predominantly associated with their host at all sites, varied by host. EMF species exhibited various dominance by site, which was consistent with three pine species, implying that they have co-migration relationships. With EMF functional complementarity, pine prefer different core EMF species to adapt environments. Abies kawakamii and T. chinensis showed similar EMF preference either the co-occurring or non-co-occurring plants, while P. morrisonicola showed unique EMF preferences, that restrict migration of A. kawakamii and T. chinensis into P. morrisonicola forest, and vice versa. The EMF range (selection) of Pinaceae plants is determined by plant phylogeny, that diverges at subfamily level. Our findings provide insights into the mechanisms of partner selection in mutualistic associations.