Se in water was determined by GFAAS and AFS. The results show that both methods have good linearity and recovery rate,also have no obvious difference,in detection limits, precision and accuracy but each have its advantages and disadvantages. The detection of GFAAS is high and the analysis is slow, usually is suitable for the determination of Se concentrations higher samples; The detection of AFS is low and the analysis speed is fast, which is usually suitable for determination of trace Se in water.