Beta diversity, which measures how species composition changes across geographic space and/or environmental gradients, has long been considered an important measure for quantifying biodiversity patterns and determining mechanisms that influence these patterns. Further, complementarity, which is essentially a measure of beta diversity, serves as the conceptual basis for systematic reserve design. Recently, beta diversity has been extended to include information on species relatedness (i.e., phylogenetic beta diversity, PBD) in three relatively distinct fields. Ecologists who study macro-organisms have started to quantify phylogenetic relatedness among assemblages to better evaluate how environmental gradients and geographic barriers influence biodiversity patterns (e.g., Graham & Fine. 2008. PBD: linking ecological and evolutionary processes across space in time. Ecol. Letters 12:1265-1277). At the same time, microbial biologists have embraced PBD, since information on relatedness but not species demarcation is readily available from the ribosomal RNA sequences that are typically used in microbial diversity assessment (e.g., Lozupone & Knight. 2005. Unifrac: A new phylogenetic method for comparing microbial communities. Appl Envrionm Microbiol 71:8228-35). Finally, conservation biologists have extended organismal based reserve design algorithms to include phylogenetic information (e.g., Ferrier et al. 2007. Using generalized dissimilarity modelling to analyze and predict patterns of beta diversity in regional biodiversity assessment. Div and Dist, 13: 252-264) in an attempt to conserve both our taxonomic and evolutionary heritage, currently and in the face of climate change. An increasing number of methodological advances and case studies are underway, in each field showing that PBD can provide new insight on mechanisms influencing biodiversity. Nonetheless, there has been limited collaboration, or even cross-citation, among these different fields. To this end we propose to bring together a diverse set of ecologists, microbiologists and conservation biologists to explore phylogenetic beta diversity, its uses, limitations and future potential as a research and conservation tool.