The Chinese mitten crab, , is an important aquaculture species in China that is widely distributed in the east Pacific coast of China, from 24°N northwards to the Korean Peninsula, 42-43°N, from 112° to 114°E. Its high market demand, favorable taste and significant advances in hatchery and grow-out techniques have resulted in this crab being cultured widely in ponds, reservoirs and lakes throughout China since the 1990s. As a consequence, aquaculture yields have steadily increased over the past decades, from 8000 t in 1991 to approximately 729900 t in 2013. The main culture areas are located in the three principal drainage basins, i.e. the Liaohe, Yellow and Yangtze Rivers. The Yangtze delta is the largest culture area among the three drainage basins. Although pond-reared populations of originated from their native habitats, i.e. the Liaohe, Yellow and Yangtze Rivers, the Yangtze population generally had the largest body size of adult crabs, the best growth performance and the best taste among three populations. Therefore, pond-reared populations of , originating from the wild Yangtze population, have become the common and major culture population in Middle and East China. Inbreeding depression and adverse selection for smaller-sized crabs eventually resulted in the genetic degeneration of pond-reared . Moreover, the blind introduction and culture of different populations of in their native habitat has led to hybrid germplasms for pond-reared populations. Previous studies have shown that wild crab seeds of juvenile showed different culture performance in ponds, and the wild crab seeds from the Yangtze River system generally had the best perform ance and attracted the highest price among these wild populations. However, to date, there is no reliable discrimination method to identify the origins of wild crab seeds from different rivers. Therefore, the current study was designed to investigate the differences and similarities of wild juvenile crabs from the three river systems. Based on morphological measures and biochemical analyses, we determined and compared the morphological parameters, hepatosomatic index (HSI), proximate composition, lipid composition and fatty acid composition of wild juvenile crabs from the three river systems. The results showed that:(1) significant differences in morphological characteristics were observed for wild juvenile crabs from the three river systems, including 12 and 18 morphological indices for female and male crabs, respectively. However, their coefficient of variation did not reach the threshold value for the subspecies. Cluster analysis showed that the wild juveniles from the Yangtze and Yellow Rivers were pooled and separated into one group, while the wild crabs from Liaohe River were divided into another group. (2) Based on the 7-10 indices with high contribution to the discrimination of wild juveniles from the three populations, different discrimination equations were established for female and male crabs of each population, respectively. The overall accuracy of discrimination was 87.5%. (3) The wild juvenile female crabs from Yangtze River had the highest HIS, while the lowest was found in the males from Liaohe River; female crabs from the Liaohe population contained higher moisture and protein levels in their hepatopancreas, while females of the Yangtze population had the lowest moisture, crude protein and carbohydrate contents. The wild crabs from Liaohe River had the highest moisture content in their body muscle, while the crabs from Yangtze River contained the highest body crude protein and total lipid contents, but the lowest carbohydrate levels. (4) For the lipid composition, except for the hepatopancreas of male crabs, the triglyceride levels in the tissues of Yangtze crabs were significantly higher than those of the other two populations, while the tissue of the Yellow River crabs had lower free fatty acid and cholesterol contents, but the highest levels of phospholipids. (5) The Yellow River crabs had the lowest levels of 18:1n9 and 18:2n6 in the hepatopancreas and body muscle, but the highest contents of 20:5n3 and 22:6n3. Overall, the hepatopancreatic differences in fatty acid composition among crabs of the three river systems were higher than those in the body muscle. In conclusion, there were significant differences in morphological indices and biochemical composition in the wild juvenile from the three river systems, which might be related to their growth environment, natural diets and heredities. These results not only provide useful information for the discrimination of wild seeds from the Liaohe, Yellow and Yangtze Rivers, but also contribute to the evaluation of wild germplasm resources and the rational utilization of natural resources of wild .