Conservation programmes that aim to protect and enhance Australia’s biodiversity have typically been focussed at the species level, but there has been a push to broaden the focus to incorporate genetic, functional, and phylogenetic diversity. Australia’s phylogenetic diversity needs protection because it contains a concentration of plant and animal lineages not found elsewhere, and is particularly vulnerable to climate change. Phylogenetic trees have become available for many organisms, but no such tree existed for Australia’s bat biota. We set out to a) construct the first comprehensive phylogeny for Australian bats and b) using this information, predict how climate-induced range shifts might impact the distribution of bat species and phylogenetic diversity by 2085. The mitochondrial cytochrome-b and nuclear RAG1 genes were sequenced for most of Australia’s bat species, and trees were reconstructed using maximum likelihood and Bayesian methods. Trees were then paired with MaxEnt species distribution models for 60 species for which adequate point location data were available for construction. The models were developed both for present-day and 2085 climatic conditions based on climate projections. Finally, present and future species and phylogenetic diversity—the summed length of the tree branches—was calculated for the entire Australian landscape. This study is the first in Oceania and Asia to establish the locations of important centres of bat diversity and to predict how that diversity might change in the future, which is key information for conserving this group.