Perchlorate and iodide concentrations were determined in brown (Undaria pinnatifida and Laminaria japonica) and red (Porphyra sp.) edible seaweeds, which are commonly consumed by Korean people, with the use of ion chromatography, coupled with a tandem mass spectrometer. Seaweeds (i.e., good sources of iodine) are among the most important plant life in the ocean and commonly consumed as food and nutritional supplement in South Korea. All seaweed samples were purchased from different regions in South Korea. The detected concentrations of perchlorate were as follows: 19.7–620.7 μg kg−1 dry weight (n = 11, mean concentration = 149.2 μg kg−1 dry weight) for L. japonica and 7.3–21.7 μg kg−1 dry weight (mean concentration = 10.6 μg kg−1 dry weight) for U. pinnatifida. Of the 11 samples of Porphyra sp., only 1 sample showed 6.7 μg kg−1 dry weight perchlorate. The concentrations of iodide in all seaweed samples varied from 0.44 to 6,800 mg kg−1 dry weight. L. japonica samples (n = 11) had significantly higher iodide concentrations, with a mean of 5,261 mg kg−1 dry weight. The bioconcentration factor values for perchlorate and iodide in the three different seaweeds varied widely and showed similar variation trends. The trend for perchlorate and iodide was Porphyra sp. < U. pinnatifida < L. japonica. The results have provided growing evidence that perchlorate frequently occurs in food products.