We estimated the population size and fishing mortality of Pacific cod Gadus macrocephalus during the spawning season in waters off Woipo, Geoje Island, Korea, using a mark-recapture method. We marked and released 51 cod>50 cm in total length; six were recaptured by local fishermen during the period from December 15 to 31, 2009. The estimated population size was ca. 180,000 and the fishing mortality of the exploitable cod was 26%. Although we could assume a closed population due to the short survey period, we evaluated the uncertainty in the estimates by applying bootstrap resampling because the sample size was small. The estimated 95% confidence interval was 94,000-568,000 for the population size and 8-49% for fishing mortality. Our study demonstrated that the application of mark-recapture methods and bootstrap resampling can be useful in stock assessment for fisheries management in Korea, but requires a larger sample size, spatially extensive coverage, and sophisticated mark-recapture models based on a refined sampling design for reliable stock assessment and biological reference points in sustainable cod management.