Abstract: A capillary electrophoresis- mass spectrometry (CE-MS) method was established for the analysis of nucleosides and related compounds in Ganoderma lucidum and G.sinense.The separation was performed in a fused silica capillary (120 cm×50 μm) at 25 °C,with 10% methanol in water containing 100 mmol/L formic acid as CE electrolyte,and 25 kV as the applied voltage were used for the separation.The optimum MS parameters were as follows:75% methanol containing 0.3% formic acid with a flow rate of 3 μL/min was selected as the sheath liquid;the flow rate and temperature of drying gas were 6 L/min and 350 °C,respectively.ESI-MS analysis was performed in the positive mode,and the full scanning range was from m/z 50 to 350.5-Chlorocytosine arabinoside was used as the internal standard.The results showed that eight investigated compounds had good linearity (R²>0.990,except guanosine) over the tested ranges.The average recoveries were between 95.3% and 104.6%.The limit of detection (LOD) and limit of quantitation (LOQ) were 0.13-9.85 μg/mL and 0.42-20.83 μg/mL,respectively.The quantification results showed that the G.lucidum contained higher total amount of nucleosides than G.sinensis.The developed CE-MS method can be applied for the analysis of nucleosides and related compounds in Ganoderma and other traditional Chinese medicines.