Incorporating phylogeny into analyses of community composition yields a holistic view of biodiversity that accounts for unequal species relatedness. Due to the constraints of evolution it is generally assumed that more closely related species will be more ecologically similar. Here we present analyses of phylogenetic diversity in California chaparral plant communities with a focus on beta-diversity (how community composition changes across a landscape). We surveyed woody plants in thirty 20 x 20 meter quadrats located in Sequoia Kings Cannon National Park and the Sierra National Forest. The geographic distance between plots varied from 20 meters to 100 kilometers. We conducted phylogenetic beta-diversity analyses by comparing the mean phylogenetic distance (MPD) between all pair-wise combinations of plots to the geographic distance between the plots. We also used the net relatedness index to identify the extent to which relatedness varied across all plots. Our results show that the MPD of woody species significantly increases with geographic distance: the classic species-level distance decay relationship was paralleled by an increase in phylogenetic diversity. Some of the quadrats were characterized by significant phylogenetic clustering or over dispersion while others were characterized by a random phylogenetic structure. These results have implications relevant to locating priority conservation areas.