Seasonal germination is critical in synchronizing seedling emergence with optimal conditions for survival but will be disrupted by climate change. Understanding how germination of threatened species with complex dormancy patterns will be affected by climate change is a priority for their management. By exploring the effects of temperature on germination for six Persoonia species ranging in rareness, this study aims to improve ex situ plant production and better understand the probable impacts of climate change on persistence of local populations. Location South‐eastern Australia. Methods The role of temperature on seed dormancy was explored using generalized additive models to predict germination probabilities for six Persoonia species ranging in rarity. Embryos were exposed to 24‐hr cycles of alternating 12‐hr warmer/light and 12‐hr cooler/dark combinations of temperatures between 8°C and 45°C. Optimal temperature conditions for germination were determined, and spatio temporal changes in germination probability were predicted in response to expected temperatures under future climate change scenarios. Results Unique germination niches representing complex responses across diurnal regimes were identified for each species. Germination probability was predicted to decline in four species in response to warmer day or night temperatures and in two species in response to cooler day or night temperatures. Across bioregions, areas of likely germination largely aligned with species‐specific temperature sensitivity, with suitable germination niche declining in four species, one staying roughly the same and one increasing in physical range under predicted climate warming. Main conclusions In response to increased temperatures associated with climate change, germination probability varied from current rates. These changes were quantified both spatially and temporally and highlight expected challenges for persistence of some populations, particularly range restricted and rare species. Current understanding of extinction threat must consider future conditions, and these results highlight the urgent need to protect populations of these six Persoonia species that are currently threatened by habitat destruction and encourage future population persistence through restoration efforts.