To understand species distributions, more knowledge is needed to elucidate the roles of how genomic variation and the impacts of biogeographic barriers shape present occurrences. The biodiversity and climatic histories of the Australian Monsoon Tropics (AMT) provides a unique system for investigating evolutionary processes. The AMT is a topographically and climatically diverse biome where well-known biogeographic barriers have been proposed as drivers of distribution patterns leading to closely-related taxa that are geographically isolated and morphologically distinct. The barriers are thought to have facilitated the large number of endemic angiosperms. However, the opposite pattern has been observed in Templetonia hookeri. It is broadly distributed across several barriers and appears to be morphologically stable across its range. Population genomic methods were used to analyze the genetic diversity and population structure of T. hookeri, and assess barrier impacts. We used a genotyping-by-sequencing (GBS) approach to assess the status of 13 populations. Results show that populations are highly isolated, are structured by geography, and inbreeding is prevalent. Genetic clustering methods also corresponded with known barriers. The significant lack of genetic diversity within populations, coupled with the support for highly structured populations, provides evidence that although populations may look similar, they are genetically distinct. This work is part of a broader project highlighting the role of AMT sandstone escarpments as habitat refugia for angiosperms during the Last Glacial Maximum, the first attempt to test for the effects of multiple biogeographic barriers across angiosperms in the AMT.