Despite growing global investments in ecosystem restoration, seed supply for native tree species remains a major bottleneck, particularly in the Global South where species diversity is high and natural seed sources dwindling due to land use change. This slows down restoration efforts and reduces their biodiversity, climate and socioeconomic benefits. We present a spatially explicit methodology for assessing the availability of site-adapted tree seed for restoration, which combines environmental clustering to define seed zones, MaxEnt species distribution models for restoration target species, and data on existing tree seed sources. Species-specific seed source gaps are identified as those zones within species' distribution ranges without any seed sources. Application of the method to 21 native pilot species in Bangladesh, India, Indonesia, and the Philippines revealed that, on average, only 34% of seed zones had designated seed sources, despite the species being widely used in restoration. An analysis of community-managed forests in Mindanao, the Philippines, showed that such forests can potentially fill the identified gaps in seed source availability, but challenges remain in registering and supporting community-managed forests as seed sources. Ninety-seven percent of the seed sources were predicted to remain within the species' suitable habitat under future climates, but the availability of sources in specific seed zones can reduce with climate change projected to shift the seed zone boundaries. The gap analysis methodology enables countries to strategically identify priority areas for seed source development. By addressing critical seed supply constraints, this approach strengthens national capacity to deliver effective, inclusive, and climate-resilient restoration at scale.