Background: Understorey vegetation is a key biodiversity component of forest ecosystems. Previous studies examined its relations with the overstorey mainly in terms of taxonomic diversity, composition or productivity. So far, none focused on the phylogenetic aspect, which represents the deepest component of diversity in a community. Here, we explored the relations between overstorey species richness and identity and the phylogenetic structure of the understorey vegetation. As a model system we used a network of 36 plots in thermophilous deciduous forests of central Italy that are part of a European project on forest biodiversity and functions. The plots, characterized by similar site conditions, represent a gradient of overstorey richness from 1 to 4-species mixtures, with variable composition. After surveying the understorey in each plot, measures of phylogenetic diversity and structure (Phylogenetic Diversity, PD; Net Relatedness Index, NRI; and Nearest Taxon Index, NTI) were calculated from a fully resolved seed-plant phylogeny obtained from a ITS-5.8S nrDNA dataset including original sequences from local plant material. Results: The resulting understorey phylogenetic tree allowed reliable estimation of PD, NRTI and NTI. Phylogenetic diversity was dependent on species richness and the strength of this relationship did not change along the gradient of overstorey tree species richness. Net Relatedness and Nearest Taxon indices were both mostly positive but nonsignificant, indicating random phylogenetic structure of the understorey. The presence of Quercus petraea, usually found in more favorable site conditions, was associated with a significant phylogenetic clustering at the species level. Conclusions: Overstorey species richness was not related to understorey phylogenetic structure, while species identity (Q. petraea) was associated with an increase in evolutionary relatedness in this forest layer, possibly due to competitive exclusion in favorable site conditions. Further studies should examine whether and how understory phylogenetic structure is affected by variables such as small scale variations in site conditions and presence of a shrub layer, both present but not accounted for in our model system. A better understanding of the role of these variables and their interaction may contribute to fill the current gap between the theoretical field of phylogenetic ecology and forest management.