The greater amberjack Seriola dumerili (Risso, 1810) is widely distributed in the tropical and subtropical waters. This fish is one of the most commercially important fishery in Asia, and also one of the upcoming new fish species in aquaculture in recent years. Even though greater amberjack is highly commercial value, studies about its biology are scarce and only few reports on catch composition or fishing round distribution. According to fishermen, there were two different phenotypes exist in the Taiwanese waters based on its habitat depth. To clarify its genetic diversity and population structure, mitochondrial COI, cytochrome
b gene and D-loop were used to analyze samples from two different morphotypes of greater amberjack. Based on principal component analysis, the morphological variations between the two morphotypes are significant, however the genetic data revealed that two morphotypes are the same population. Although the genetical and morphological data were not consistent, the greater amberjack caught from Taiwanese water is a single population. In the future, we will continue to cooperate with Nagasaki University in Japan to develop higher-resolution DNA markers in order to further clarify the differences between the two groups