Seafood inspection and certification has become a trend on international trade. Recent incidences of chemical residues were examined in exporting seafood products which hinder the future export to the European Union and Japan particularly. Hence, the perceptions of seafood quality and safety from a consumer point of view and international trade concerns are becoming important. In fact, seafood inspection and certification are set into action on the world gradually. It is clear that international legislation is moving toward to make HACCP as a mandatory requirement for the food industry. In this study, questionnaire was designed to explore the perception of Taiwanese consumers about food safety and issues related to the HACCP system in the industry. An econometric Logit model was applied to estimate relationships between perceptions of food safety and seafood consumption in Taiwan. The empirical results show there are significant differences in perceptions regarding the characteristic of gender, education, income, eating location and buyer. The empirical results indicate that, consumer would like to pay more (average 7.81% of current price) for certified seafood due to safety concerns and time saving, but part of producers worry the increasing cost when apply the HACCP system. It also implies incentives of guidance and assistance provided by government is needed in the initial stage.