We report the results of molecular monitoring of ‘whalemeat’ markets in the Republic of (South) Korea based on nine systematic surveys from February 2003 to February 2005. As Korea has no programme of commercial or scientific whaling and there is a closure on the hunting of dolphins and porpoises, the only legal source of these products was assumed to be incidental fisheries mortalities (‘bycatch’) as reported by the government to the International Whaling Commission. Species identification of 357 products using mitochondrial DNA control region or cytochrome b sequences and the web-based programme DNA-surveillance revealed three species of baleen whales (North Pacific minke, common form Bryde's and humpback), three species of beaked whales (Cuvier's, Stejneger's and Blainville's), seven species of dolphins (short-finned pilot, false killer and killer whales; Risso's, bottlenose, common and Pacific white-sided dolphins) and two species of porpoises (harbour and finless). Comparison of market products with official records revealed a number of discrepancies. Of the eight species identified on the markets in 2003, three were not reported in official records for that year. Of the 11 species identified in 2004, five were not reported as bycatch, although one species, a humpback whale, was reported as ‘stranded’. We also found significant inconsistencies in the expected frequencies of products from most species, including a large over-representation of finless porpoises and false killer whales. We suggest ways in which market surveys could be improved to provide better information on the magnitude of fisheries bycatch and other illegal, unregulated and unreported (IUU) exploitation of wildlife.