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Karst regions are characterized by unique geological formations that pose challenges to soil fertility and plant nutrition. In this study, we investigated the distribution and interactions of selenium (Se) in soils of Zheng'an County, a representative karst region in subtropical China. The results showed that the Se enrichment in the soils of Zheng'an County was high, with total contents ranging from 0.49 to 3.87 mg/kg and an average of 1.22 mg/kg, making the area Se-rich. Despite the abundance of Se, the effective percentage of Se uptake by plants was relatively low due to the generally moderately acidic nature of the soils in the region (pH: 5.98–6.60), which encourages the conversion of the available Se into forms that are not readily accessible. In addition, the high organic matter (OM) content (21.92–127.66 g/kg) promoted Se retention by interacting with Ca2+ in carbonate rocks. In addition, the clay content (50.73% to 76.19%) enhanced Se adsorption and limited Se availability. In conclusion, this study provides a basis for soil management and ecological restoration strategies in karst landscapes, highlights new insights into the dynamics of Se, and calls for further research to elucidate the Se availability mechanism and improve the efficiency of Se uptake by plants. Meanwhile, this study provides the first systematic study of Se transport and transformation, as well as Se-enriched Gastrodia elata in karst regions, and provides a preliminary understanding of the geochemical behavior of Se in karst regions. [ABSTRACT FROM AUTHOR]