This study aimed to empirically investigate the applicability of ecosystem-based TAC (Total Allowable Catch) fisheries management targeting the large purse seine fishery where multi-species are regulated by TAC. Using a linear programming, the optimal fishing effort and the catch amount by species which maximize fishing profits were analyzed under the constraint condition of catch limits by species. Analytical results showed that an application of TAC on only chub mackerel would have negative impacts on fish stocks such as hairtail and jack mackerel by increasing the level of fishing effort to achieve its allocated catch limit. However, under the constraint condition of catch limits of all species, it was shown that optimal catches of all species were achieved within their catch limits. It implies the importance of ecosystem-based management considering biological and technical interactions of species those were excluded in the traditional single species fisheries management.