The swimming crab is an important commercial fishery species in China, Korea and Japan. Overfishing and destruction of habitats in coastal waters mean that the natural resources cannot meet the swimming crab’s increased demands for food, caused by large-scale stock enhancement in Liaoning, China over the last eight years. The genetic response of the local wild populations to such a large-scale release has not been investigated. Here, we monitored the temporal variations in genetic diversity and structure in Panjin and Yingkou using eighteen microsatellite markers across six years. A high level of genetic diversity was maintained in these populations, but significant deviation from HWE was observed (P < 0.05). The F_is was positive. Genetic diversity indices were not stable and fluctuations were particularly apparent in the temporal Panjin population. The genetic differentiation was low but such fluctuations or differences exhibited in the genetic architecture may reflect the interactions between the crab life cycle and intensive anthropogenic manipulations. Our results strongly inferred that large-scale stock enhancement of the swimming crab altered the genetic status of the local population structure. Several suggestions have been proposed to achieve successful stock enhancement.