Microbially mediated plant-soil feedbacks drive patterns of plant growth, competitive ability, succession, and community composition. Although rare plant species maintain unique functional traits that often facilitate negative feedbacks, there is not a consensus on the belowground drivers nor the effects of phylogenetic origin of previously plant-conditioned soil on aboveground traits associated with rare species. Using a common garden, we connect belowground fungal colonization to aboveground traits in species varying in rarity, and soil conditions varying in the phylogenetic relatedness of conditioning plant species, to demonstrate the mechanistic relationship between belowground ectomycorrhizal fungal (ECM) colonization and aboveground total plant biomass in 14 Eucalyptus species varying in their rarity status. Specifically, we found that while the rarest species displayed 88% less total biomass than common species, the rarest species also maintained 62% greater ECM colonization than common counterparts. Further, negative feedbacks resulted in reduced biomass coupled with positive feedbacks that resulted in increased ECM colonization that varied on the basis of phylogenetic relatedness. The rarest species decreased by 71% - 94% in total biomass but increased by 96% - 114% in ECM colonization in phylogenetically similar and distant soil compared to conspecific soil conditions. The effect size of ECM colonization directly affected the effect size of total biomass in phylogenetically distant conditions with a significant negative correlation (r^2 = -0.83) to show that biomass may be a function of ECM colonization acting differently among species varying in rarity. Consequently, rare plant species may utilize stronger associations with belowground mycorrhizal mutualists than common plant species, to facilitate geographic, competitive, and functional persistence, even while maintaining lower biomass.