Genetic evidence for speciation in Japanese sand lance Ammodytes personatus: Pleistocene isolation, temperature and current promoted speciation Zhqiang Han1,2, Zhiyong Wang3, Takashi Yanagimoto4 and Tianxiang Gao1,2 1 Fishery College, Zhejiang Ocean University, Zhoushan, PR China E-mail: gaotianxiang0611@163.com 2 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China 3 Fishery College, Jimei Universtiy, Xiamen, PR China 4 National Research Institute of Fisheries Science, Yokohama, Japan Two divergent sympatric mtDNA lineages have been described in Japanese sand lance Ammodytes personatus, and this high inter-lineage divergence raises questions about the taxonomic status of A. personatus lineages in the Northwestern Pacific. In the present study, AFLP markers were used to analyze the genetic structures of A. personatus and the status of the two mtDNA lineages. Two hundred and eleven individuals of A. personatus and 37 individuals of Ammodytes hexapterus were amplified by four primer combinations. The results showed a north geographic group and a south geographic group that were reciprocally monophyletic. Complete reproductive isolation may exist between the two geographic groups. These results suggest that the two groups have already reached a stage of sufficient genetic differentiation to be considered as two distinct species. The incongruence between nuclear groups and mitochondrial lineages suggests the two distinct lineages do not represent cryptic species and the presence of divergent mitochondrial lineages in the same sample is a result of secondary contact after an extended period of isolation. The Pleistocene isolation and the biological characteristics of species may be responsible for speciation in A. personatus.