Understanding how evolutionary history is distributed across plant diversity darkspots is essential for conserving global biodiversity, yet such knowledge is limited for much of tropical Southeast Asia. Here, we present the first nationwide, spatially explicit assessment of phylogenetic diversity (PD) and phylogenetic endemism (PE) for Myanmar's vascular plant diversity, integrating species distribution models with a dated megaphylogeny encompassing 4943 species. Using binary habitat suitability predictions for 2453 modeled species, we map evolutionary diversity while minimizing biases arising from uneven sampling. Central Myanmar, characterized by seasonally hot and dry environments, exhibits relatively high PD and PE despite moderate species richness. Using Categorical Analysis of Neo- and Paleo-Endemism (CANAPE), we also distinguish between paleo-endemism, representing areas dominated by ancient and geographically restricted lineages, and neoendemism, reflecting regions shaped by recent diversification. Paleo-endemism is most concentrated in warm, fragmented western and central mountain systems functioning as long-term refugia (∼21,976 km²), and neoendemism is clustered in cool, topographically complex northern montane regions shaped by recent diversification (∼31,230 km²). Current protected areas encompass 58.63% of neoendemic regions (∼18,365 km²) but only 6.95% of paleo-endemic regions (∼1513 km²), indicating that a large share of Myanmar's irreplaceable evolutionary history remains unprotected. Identifying priority areas encompassing PD and PE hotspots, as well as centres of neo- and paleo-endemism within Permanent Forest Estates (PFEs), could increase the proportion of these priority areas covered by protected areas from 6.42% under the existing network to 15.11% under the proposed conservation expansion. Our findings demonstrate that evolutionary diversity in Myanmar is governed by the interaction of climate, environmental heterogeneity, and historical stability, and establish a critical evolutionary baseline for conservation planning in one of the world's most underexplored floristic hotspot regions.