A new species, Pseudodiaptomus koreanus sp. nov. (Calanoida, Pseudodiaptomidae), which has so far been identified as P. inopinus Burckhardt, 1913, is described from Korean estuaries. This new species differs from P. inopinus in the broad and short posterior process of the female genital flap, rounded posteriocentral projection between the gonopores, presence of a posterodorsal spinule on the fifth pediger of the male, and a row of fine ventral spinules on the male second urosomite. The new species is also distinguishable from P. nansei Sakaguchi and Ueda, 2010 by the presence of a row of fine spinules along posterior margins of the second and third pedigers in both sexes, rounded posteromedial projection between the gonopores, separation of ancestral segment XXI and compound segments XXII-XXIII of the male right antennules, and a row of fine ventral spinules on the male second urosomite. Their ribosomal internal transcribed spacer 1 (ITS 1) and mitochondrial gene cytochrome oxidase subunit I (mtCOI) sequences supported the conclusion based on morphological data, with considerable divergence values between P. koreanus and P. inopinus: 12-14% for ITS 1 and 14-22% for mtCOI. The ITS 1 and mtCOI sequences of specimens of two morphs of P. koreanus with different male fifth legs differed by <1.2% for ITS1 and <3.5% for mtCOI, suggesting that these morphological differences represent interspecific variability.