Objective To establish an analytical method of the endosulfan concentrations （α-endosulfan and β-endosulfan） in biological samples by GC-MS/MS. To observe the distribution of endosulfan in aquatic animals and provide experimental evidence for forensic identification of relevant cases. Methods Acetonitrile was added to the blood and muscle samples for precipitating the protein. The endosulfan concentrations were determined by GC-MS/MS in multiple reaction monitoring mode. Qualitative analysis was performed according to the retention time and ion rate, and quantitative analysis was performed by external standard working curve method. Results In blood samples, the calibration curves of α-endosulfan and β-endosulfan ranging from 0.062 5 to 10 μg/mL had good linear relationship, the correlation coefficients （r） of which were >0.99. The limits of detection （LOD） were 1 ng/mL and 2 ng/mL and the limits of quantification （LOQ） were 4 ng/mL and 8 ng/mL, respectively. In muscle samples, the calibration curves of α-endosulfan and β-endosulfan ranging from 0.062 5 to 10 μg/g, the r of which were >0.98. The LOD were 1 ng/g and 4 ng/g and the LOQ were 4 ng/g and 16 ng/g, respectively. The accuracy of α-endosulfan and β-endosulfan was 90.76%-108.91% both in blood and muscle samples, the interday and intraday precision were 2.35%-8.71% and 5.44%-10.29%, respectively. In poisoning cases, endosulfan were detected in all parts of fish and crab and the content difference was statistically significant. Conclusion The endosulfan detection method based on GC-MS/MS established in the present study is rapid, sensitive and accurate, which can be applied to the endosulfan detection in traces biological samples. The distribution of endosulfan in fish and crab was different, which can provide evidence to the sample collection and analysis for toxicological analysis in relevant forensic identification.