Object To study the different fingerprints of hydrophilic and hydrophobic components in roots of Salvia miltiorrhiza Bge. collected from different habitats, and discovery the relationship between the two types of components. Methods The fingerprints were detected by RP-HPLC and the results were analyzed by SPSS software. Results Roots of S. miltiorrhiza collected from different habitats showed different fingerprints of hydrophilic and hydrophobic components, there is no obvious relationship between the two types of components. Conclusion In order to control the quality of 5. miltiorrhiza roots that is used to manufacture injections, we must assay the hydrophilic components, such as salvianolic acid B should be determinded.