The structure of the real ecological networks is determined by multiple factors including neutral processes, the relative abundances of species, and the phylogenetic relationships of the interacting species. Previous efforts directed to analyze the relative contribution of these factors to network structure have not been able to fully incorporate the phylogenetic relationships between the interacting species. This limitation stems from the difficulty of predicting interaction probabilities based on the independent phylogenies of interacting species (e.g. plants and animals). This is not the case for plant facilitation networks, where nurse and facilitated species evolve in a common phylogeny (e.g. spermatophyte phylogeny). Facilitation networks are characterized by both high nestedness and interactions tending to occur between distantly related nurse and facilitated species. We evaluate the relative contribution of phylogeny and species abundance to explain both the frequency of observed interactions as well as the network structure in a real plant facilitation network at Tehuacán Valley (central Mexico). Our results show that the combined effects of phylogeny and species abundance were, by far, the best predictors of both the frequency of the interactions observed in this community and the parameters (nestedness and connectance) defining the network structure. This finding indicates that species interact proportionally to both their phylogenetic distances and abundances simultaneously. In short, the phylogenetic history of species, acting together with other ecological factors, has a pervasive influence in the structure of ecological networks.