A capillary electrophoresis (CE) method was developed for the simple and highly-sensitive determination of iodine species in seawater. The proposed method is based on the on-capillary preconcentration of iodide and iodate using the principle of transient isotachophoresis (tITP) stacking, and direct UV detection of the separated species at 226 and 210 nm, respectively. The preconcentration procedure takes advantage of the electrokinetic introduction of the terminating ion [2-( N-morpholino)ethanesulfonate (MES)] into the capillary, that enables a longer tITP state. The appropriate conditions for the tITP step were optimized by varying the MES and sample injection time and the concentration of cetyltrimethylammonium chloride (CTAC). The latter component of the separation electrolyte (SE) was shown to strongly affect the migration and therefore the enrichment of iodide due to specific ion-association. The optimized separations were performed in 12.5 mM CTAC, 0.5 M NaCl (pH 2.4). Valid calibration is demonstrated in the range 3-60 microg x L(-1) iodide ( R=0.9992) and 40-800 microg x L(-1) iodate ( R=0.9994). The detection limits achieved were 0.23 microg x L(-1) (2 nM) for iodide and 10 microg x L(-1) (57 nM) for iodate. Such sensitivity and linearity thresholds allowed the reported tITP-CE system to be applied to direct speciation analysis of surface and seabed seawater. The comparison of CE results with those of an ion-chromatography (IC) technique proved that the method has acceptable accuracy.