Natural karst forests can support very high level of biodiversity, but difference of species diversity between the natural karst forests and non-karst forests is still less concerned. To analyze the difference of species diversity of the natural karst forests and non-karst forests in subtropics, we made a census of all woody species with diameter at breast height (dbh)≥1 cm in a 1-ha plot in Mulun subtropical karst forests and a 1-ha plot in Maoershan subtropical non-karst forests, Guangxi of south-western China. Species richness in Mulun plot (120 species) was higher than that in Maoershan plot (116 species). Mulun plot contained more families and genera, more stems and a larger proportion of rare species (species of individuals less than or equal to 1 ha^-1). At smaller scale (<4000 m²), species accumulation rate in Mulun plot was lower than that in Maoershan plot, and it was reversed at larger scale (>5000 m²). Total basal area in Mulun plot (18.47 m²) was smaller than that in Maoershan plot (30.74 m²). Size structure distribution of all woody species in the two plots showed insignificant difference. The ten most dominant species, families and genera were quite different in the two plots. In Mulun plot, the most important species and family were Sinosideroxylon wightianum and Sapindaceae, while in Maoershan plot, Castanopsis carlesii and Fagaceae were the most important species and family. All these results suggest that middle subtropical natural karst forest in Mulun supports diverse species with high spatial variability, and their species composition are quite different with non-karst forests. This study implies that special attention is needed on selecting suitable species in karst forest restoration and vegetation management strategies.