Mexico is a center of diversity for pines, but few studies have examined the ectomycorrhizal (ECM) fungal communities associated with pines in this country. We investigated the ECM communities associated with Pinus montezumae seedlings and mature trees in neotropical forests of central Mexico and compared their structure and species composition. Root tips were sampled on both planted seedlings and naturally occurring adult trees. A total of 42 ECM operational taxonomic units (OTUs) was found on P. montezumae. Diversity and similarity indices showed that community structure was similar for both plant growth stages, but phylogenetic diversity and Chao-estimated richness were higher for seedlings. Species composition differed between communities. The dominant OTUs belonged to the families Atheliaceae, Cortinariaceae, and Sebacinaceae, although different taxa appeared to colonize seedlings and adults. Only 12 OTUs were shared between seedlings and adults, which suggests that ECM fungi which colonize seedlings are still not fully incorporated into mycelial networks and that ECM taxa colonizing young individuals of P. montezumae are likely to come from fungal propagules. Intra-generic diversity could be an insurance mechanism to maintain forest productivity under stressed conditions. This is the first report describing the abundance of Atheliaceae in tree roots in neotropical ecosystems.