This article describes an on-line technique for hydrodynamic injections of long sample plugs with simultaneous stacking of iodine species in capillary electrophoresis (CE) with diode array detection. Surfactant-coated multiwalled carbon nanotubes (SC-MWNTs) were used as a pseudostationary phase for the separation of iodate, tetraiodothyronine,triiodothyronine, diiodothyronine, and diiodotyrosine. The effects of MWNTs, concentration of SCMWNTs and salt, of buffer pH value, injection times were examined. Under the optimized conditions, i.e. detection at 230 nm, a separation voltage 25 kV, a borate running buffer of pH 7.5 and a SC-MWNT concentration of 9 μg · mL −1 , the method gave relative standard deviations of the retention times and peak areas in intra-day assays (for n = 6) and for inter-day assays (for n = 3) of less than 4.49 and 5.80 %, respectively. The CE method was then applied to the analysis of the above iodine species in (spiked) kelp (kunbu) and porphyra, and recoveries ranged from 81.6 to 98.4 % with RSDs (n = 3) for extraction repeatability of <3.39 % in all cases.