Abstract: Recently, differentiation in phenotypic traits (P_ST) and differentiation at neutral molecular markers (F_ST) across populations have been become an important topic in evolutionary biology. The Minjiang River is a key genetic introgression zone between the Chinese mitten crab (Eriocheir sinensis) and the Hepu mitten crab (Eriocheir hepuensis), making it an excellent area to study their genetics and evolutionary mechanisms. We compared and analyzed P_ST in 14 phenotypic traits and F_ST in six microsatellite markers from 133 individuals of the mitten crab, sampled in the Minjiang River in 2009 and 2010. The results indicated that 11 phenotypic traits were significantly different (P<0.01) between the 2009 and 2010 populations. The mean expected heterozygosity (H_E) of the 2009 populations was significantly higher (P=0.008) than that of 2010 populations, but the mean allele richness (AR), observed heterozygosity (HO) and inbreeding coefficient (FIS) were all not significant between 2009 and 2010 populations (P=0.136-0.675). F_ST in microsatellite markers was 0.1429 between the two years. In the 14 traits, only one trait (F2) was found with P_STST, suggesting that stabilizing selection is favoring a trait of F2; the other 13 traits were P_ST>F_ST, suggesting that directional selection is occurring. This study provides valuable data to the further study and analysis of the molecular evolution of the mitten crab, and contributes a useful reference in comparing P_ST and F_ST in other aquatic organisms.