Abstract: In the current study, the nine elements in the otolith core elements（Sr, Ba, Mg,Na, Si, Cr, Mn, Ca, Zn）of young-of-the-year （YOY） silver carp collected during August-September of 2012, 2014, and 2016 from the Yangtze River and Ganjiang River were analyzed using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). It was showed that the ratios of the four trace elements to the calcium (Sr∶Ca, Ba∶Ca, Si∶Ca, Mg∶Ca) in the otolith core of the YOY silver carp in Yangtze River and Ganjiang River was basically unchanged among the three years from the same river. However, there was a significant difference between the two stocks from Yangtze River and Ganjiang River and the ratios of Si∶Ca and Sr∶Ca made the greatest contribution to stock identification. According to the linear discriminant analysis (LDFA) of the four element ratios, the overall classification accuracy rate of Yangtze River silver carp stock was 92.11%, and the classification accuracy rates in 2012, 2014 and 2016 were 92.31%, 93.33% and 90.91%, respectively. The overall classification accuracy rate of Ganjiang River silver carp stock was 92.31% and the classification accuracy rates in 2012, 2014 and 2016 were 80.00%, 96.77% and 93.75%, respectively. Thus, the four element ratios in otolith core could be used as elemental fingerprints to identify silver carp stocks from the Yangtze River and Ganjiang River. Analysis of otolith microchemistry by LA-ICP-MS will be an effective technique in stock discrimination such as silver carp from Yangtze River and Ganjiang River.