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Largemouth bronze gudgeon (Coreius guichenoti) is an endemic freshwater fish in the upper reaches of the Yangtze river in China (Ding 1994). As a typical migratory river fish, broodstocks of C. guichenoti spawn in the middle and lower reaches of the Jinsha river, which is part of the upper reaches of the Yangtze river. The eggs hatch in the process of drifting downstream, then the juvenile fish is traced towards upstream of the Yangtze river to spawn (Cao 2008). The impoundment of Xiangjia dam in 2012 and Xiluodu dam in 2013 on the lower reaches of the Jinsha river have blocked the migration routes of C. guichenoti supplementary stocks because of which the number of broodstocks declined significantly. Artificial propagation of C. guichenoti has been developed to conserve the resources. Besides increasing the number ofC. guichenoti populations, maintaining the genetic diversity of populations should also be concerned in the conservation strategy. To date, 29 polymorphic microsatellites have been published for C. guichenoti, and 25 of their motifs are dinucleotide repeats (Liao et al. 2007; Xu et al. 2007). Genetic diversity in seven populations of C. guichenoti has been examined using 11 loci isolated by Liao et al. (2006, 2007). Dramatic population differentiation among populations which were seperated by dams was observed (Zhang and Tan 2010). No significant variation occurred among populations in continuous habitat (Zhang and Tan 2010), which was consistent with the study by Yuan et al. (2008). Therefore it is necessary to analyse the genetic diversity of populations seperated by Xiangjia dam and Xiluodu dam. Dinucleotide microsatellites have been demonstrated to be less polymorphic and stable than trinucleotide and