Accurate knowledge of the distribution patterns and environmental determinants of threatened plants is essential for effective conservation prioritization. We conducted a regional assessment of nationally protected gymnosperms in Guangxi, southern China, a karst-dominated region spanning tropical– subtropical climatic transitions. Based on 213 georeferenced records for 35 taxa (6 families, 15 genera), we examined species richness, elevational patterns, and climatic associations at a regional scale across Guangxi (using a 50 km × 50 km spatial grid). Of these taxa, 15 are listed as national Class I protected species and 22 are categorized as Critically Endangered (CR), Endangered (EN), or Vulnerable (VU) according to the IUCN Red List, with most showing declining global population trends. Two Guangxi endemics and 11 karst-obligate species indicate high conservation irreplaceability. Species richness was concentrated in the central-northern Guilin–Liuzhou karst corridor and southwestern border regions, with a maximum of 13 taxa per 50-km grid cell. Occurrences were strongly biased toward low elevations, with 50.2% of records below 200 m. Principal component analysis identified temperature, particularly winter minimum temperature and seasonality, as the dominant environmental gradient (46.88% of explained variance), followed by precipitation-related factors (26.58%). These patterns, together with severe habitat fragmentation and anthropogenic pressures in lowland karst landscapes, underscore the urgent need for spatially targeted, climate-informed conservation actions in this globally important biodiversity region.