In this study, the differences of institutional development processes of fishery products wholesale markets were compared between Korea and Japan in order to suggest improvement direction of trading system in Korea. The wholesale markets have shrunk while wholesale and distribution has been becoming larger in size in both countries. A summary of differences in the wholesale market trading systems between Korea and Japan is as follows: first, middle wholesalers play pivotal roles in wholesale transaction in Korea, and wholesale corporations take such roles in Japan. Second, most wholesale corporations take charge of listing in Korea whereas such corporations are in charge of buying in Japan. Third, Korea has high proportion of auction for transactions, in contrast to Japan with high proportion of relative transactions. Forth, Korea maintains more sales within the wholesale markers and has more small and medium customers than Japan. Finally, Korea investigates inside causes to find solutions for the decreased competitive power of the wholesale market, whereas Japan copes with the problem by searching for outside customers. To seek solutions for the decreased competitiveness of Korean fishery products wholesale markets, middle wholesalers’ consignment should be limitedly allowed, and improvement direction of wholesale corporations should be investigated in the future study.