Most rare and endangered Gymnosperms in karst regions are restricted to mountaintop habitats with inferior conditions and require urgent protection. However, in the literature there is a lack of information about the plant community structure of biotic communities in these ecosystems, which could be used to inform conservation efforts. Here a plant community typical of endangered Gymnosperms in the Mulun karst forest was selected for investigating plant community structure and microtopography. Spatial variability of plant community characteristics was studied using geo-statistical techniques, and the correlations between community characteristics and topographic factors were analysed. The results indicated a complex community structure of 73 species belonging to 39 families and 58 genera, with 3, 67, and 3 species representing Gymnosperms, Dicotyledons, and Monocotyledons, respectively. Dominant families were Fagaceae, Rosaceae and Lauraceae, containing more than five species each. About 64.1% of all families and 81.0% of all genera were represented by only one species. Focussing on Dicotyledoneae, the net relatedness index (NRI) and nearest taxon index (NTI) of this class indicated a random phylogenetic community structure. The individual number, total basal area of all species (BA) and the NTI had strong spatial correlations, at 5.66 m, 4.75 m, and 6.51 m, respectively, showing relatively small ranges of spatial continuity. Shannon's diversity index, Simpson's diversity index, and Pielou's evenness index had strong spatial correlations, at 71.01 m, 71.01 m, and 42.44 m, respectively, showing relatively large ranges of spatial continuity. There were significantly positive correlations between BA and convexity, and between relative basal area of endangered Gymnosperms and slope degree. NTI showed a extremely significant positive correlation with relative elevation, and significantly negative correlations with both slope aspect and slope degree. These results provide useful information for conservation and restoration efforts for endangered Gymnosperm species in karst regions.