Identifying hotspots of particularly rich or localised biodiversity is key strategy for prioritising areas for protection and management. However, different biodiversity measures may lead to the prioritisation of different areas for conservation. Here we use species distribution modelling and spatial biodiversity analyses to map and compare hotspots of Australian subtropical rainforest reptile and amphibian diversity identified using three biodiversity measures - Alpha Diversity, Weighted Endemism, and Corrected Weighted Endemism. Spatial patterns of frog and reptile diversity largely correlate with each other, and with previous studies in plants and other vertebrates, with diversity and endemism both concentrated in montane uplands and correlated with paleoclimatic stability. However Corrected Weighted Endemism highlights additional peripheral hotspots of Short-Range Endemic taxa away from Alpha Diversity hotspots, especially in the poorly known ‘vine-thicket’ habitats of mid-east Queensland. Spatial analyses of the overlap of burn scars from two recent massive fire events show that many of these peripheral hotspots may have been impacted, further highlighting these areas as a priority for targeted survey and conservation assessment.