Bull. Jpn. Soc. Fish. Oceanogr. 73(1), Page 16-21, 2009   Genetic identity between two types of Japanese anchovy, Engraulis japonicus, from Sagami Bay based on the mitochondrial cytochrome b gene Hisashi Nakategawa1†, Keitaro Dairiki2‡, Shiro Itoi2, Haruo Sugita2 and Seiji Akimoto3 1 Kanagawa Prefectural Fisheries Technology Center, Miura, Kanagawa 238-0237, Japan 2 Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-8510, Japan 3 Fisheries Division, Environment and Agriculture Department, Kanagawa Prefectural Government, Yokohama 231-8588, Japan † e-mail: nakategawa.bayg@pref.kanagawa.jp ‡ Present address: Saitama Prefecture Agriculture and Forestry Research Center Fisheries Laboratory, Kazo, Saitama 347-0011, Japan Japanese anchovy Engraulis japonicus was abundantly caught by various catching methods such as large size set-net in Sagami Bay, Japan. The anchovy with fat and slightly short body have been observed in the catch of the fish, especially in the coastal area of east Sagami Bay since 2005. The specimens with condition factor (CF)10 were represented as fat type, whereas those with CF<10 were represented as normal type in this study. The formers were caught mostly in early spring, and the catch of the type sometimes reached the half of the total catch of the fish. We investigated the genetic difference in cytochrome b gene on mitochondrial DNA between fat and normal types of anchovy classified by morphological characters. Difference in nucleotide diversities within each type was not observed between two types, and the net sequence divergence and pair-wise fixation index (FST) between two types were very low, suggesting no genetic heterogeneity. The phylogenetic tree based on the partial sequences of cytochrome b gene also demonstrated that two types of anchovy formed a cluster with E. japonicus. In the samples collected in Sagami Bay from January 2005 to July 2007, the distribution of CF for fat type was not clearly separated from that for normal counterpart. These results suggested that the morphological variation of the anchovy E. japonicus was due to the difference in their migration pattern and food environments. Key words: Engraulis japonicus, genetic difference, mtDNA, cytochrome b, condition factor, Sagami Bay