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Abstract Distribution models are widely used to understand landscape biodiversity patterns, facilitate evolutionary and ecological studies, and for making informed conservation decisions. While it is common to examine consequences of climate change, impacts of land use on distributions, a major factor in limiting ranges and corridors between populations, are less well understood. Here, we use distribution models to quantify changes in biodiversity due to land use for Michigan floral assemblages. We leveraged a distribution model dataset (1930 species) integrated with dated phylogenetic information and USGS land use maps to parse Michigan areas with unsuitable habitat. Additionally, we quantify the degree of high-quality habitat lost for each species, identifying those most strongly impacted by land use changes. Approx. 39% of Michigan terrestrial habitat fell within “unsuitable” land use categories. Sites predicted to harbor the most species based on climatic variables were those sites that lost the greatest proportion due to land use changes. Further, excluded sites were preferentially those composed of more phylogenetically even communities. Overall, the impact of land use changes on community species richness was the preferential loss of sites with the predicted highest biodiversity. For phylodiversity metrics, land use changes increased the degree of community phylogenetic clustering. This results in overall decreased phylodiversity, leading to assemblages less equipped to respond to rapid climatic changes. Our results confirm land use to be a major, but somewhat overlooked, factor impacting local diversity dynamics and illustrate how local-scale land use impacts regional-scale richness and phylodiversity patterns, likely leading to increased community fragility.