A new method for speciation analysis of two inorganic selenium species was developed by on-line coupling of capillary electrophoresis (CE) with hydride generation-atomic fluorescence spectrometry (HG-AFS) and on-line conversion of Se(VI) to Se(IV). Baseline separation of Se(VI) and Se(IV) was achieved by CE in a 50 cm x 75 microm inside diameter (ID) fused-silica capillary at -20 kV using a mixture of 15 mmol.L(-1) NaH2PO4 and 0.5 mmol.L(-1) cetyltrimethylammonium bromide (pH 7.5) as electrolyte buffer. Se(VI) was on-line reduced to Se(IV) by mixing the CE effluent with concentrated HCl. The precision (relative standard deviation, RSD, n=7) ranged from 0.7 to 1.3% for migration time, 6.4 to 3.7% for peak height response, and 5.9 to 6.1% for peak area for the two selenium species at the 500 microg.L(-1) (as Se) level. The detection limits were 33 and 25 microg.L(-1) (as Se) for Se(VI) and Se(IV), respectively. The recoveries of the two selenium species in five locally collected water samples ranged from 88 to 114%. The developed method was applied to speciation analysis of inorganic selenium species in spiked natural water samples.