1. Phylogenies are increasingly incorporated into ecological studies on the basis that evolutionary relatedness broadly correlates with trait similarity. However, phylogenetic approaches have rarely been applied to monitoring long-term community change or guiding management. 2. We analysed a 25-year resampling data set (1976-2001) of 41 tallgrass prairie remnants (Illinois, USA) to test for phylogenetic signals of plant community structure, change, environmental associations, fire management and functional traits. A community phylogeny was constructed using GenBank sequences, and trait data were acquired from the TRY consortium. Phylogenetic measures of alpha and beta diversity were compared with taxonomic and functional measures. 3. From 1976 to 2001, communities became more phylogenetically clustered relative to null model expectations, that is increasingly restricted to subsets of species more closely related than expected by chance. Phylogeny was a sensitive indicator of environmental gradients and fire management. There were strong relationships between phylogeny and traits: key traits were phylogenetically non-random and phylogenetic diversity was a necessary complement to species richness for explaining variation in trait diversity. 4. Phylogeny revealed a shift in community structure over time, with sites having been phylogenetically random in 1976 but becoming differentiated from each other by 2001. In contrast, measures of taxonomic and functional diversity showed differentiation at both time points. Phylogenetic patterns likely reflected changes in species' abundances mediated by the influence of environmental conditions and fire frequency.5. Synthesis and applications. Phylogenetic analyses can elucidate factors central to sound monitoring and management of plant communities. In this system, phylogeny was not a proxy for other indicators, but provided information complementing taxonomic-based and trait-based approaches for understanding vegetation structure, change and response to fire management. Phylogenetic approaches to ecological analysis are increasingly accessible, but fuller understanding of phylogeny-trait relationships and further development of user-friendly analytical tools are needed for phylogenetics to widely inform restoration and management. In some systems, targeting phylogenetic diversity may be an effective means for restoring functionally diverse plant communities. Phylogenetic analyses can elucidate factors central to sound monitoring and management of plant communities. In this system, phylogeny was not a proxy for other indicators, but provided information complementing taxonomic-based and trait-based approaches for understanding vegetation structure, change and response to fire management. Phylogenetic approaches to ecological analysis are increasingly accessible, but fuller understanding of phylogeny-trait relationships and further development of user-friendly analytical tools are needed for phylogenetics to widely inform restoration and management. In some systems, targeting phylogenetic diversity may be an effective means for restoring functionally diverse plant communities. © 2015 The Authors. Journal of Applied Ecology © 2015 British Ecological Society