Purpose The karst region in southwestern China is undergoing soil erosion and rocky desertification. The different silicon (Si) fractions along the hillslopes in this mountainous region could benefit plant growth and alleviate the ecological deterioration. However, extensive distribution of carbonate rocks may lead to limited plant available Si. The mountainous terrain in karst region also leads to more Si output, which seriously affects the biogeochemical cycle of Si in this area. Yet, the soil Si fractions in the karst region have not been fully evaluated. Methods Soil profiles and their corresponding plants were sampled from two typical karst mountains in Guizhou, China. The different fractions of non-crystalline Si in soil, accounting for the most important pool for Si availability to plants, were analyzed by the improved sequential chemical extraction and Si concentrations in plants grown in this region were also measured. Results The concentration and storage of non-crystalline Si were higher at lower slopes (storage was 2.44, 2.73, and 3.25 kg center dot m(-2) for upper, middle, and lower slopes, respectively) than other slope positions. Grasses dominated at lower slopes and contained significantly higher Si (mean +/- SD: 14.42 +/- 6.63 mg center dot g(-1)) than trees and shrubs (1.94 +/- 1.78 and 1.29 +/- 1.00 mg center dot g(-1), respectively), which were primarily distributed on upper slopes. However, Si concentrations of the same plant species in different slope positions had no significant correlation with soil acid Na acetate-Si, the Si regarded as directly available for plants. Conclusions This study suggests that plant species and soil properties have a significant impact on the soil Si distribution of hillslopes in karst region. Soil erosion may decrease non-crystalline Si concentrations in soils and impair Si uptake in grasses, which need to be considered in ecosystem management in this region.