Large yellow croaker (Larimichthys crocea) is an important commercial marine fish endemic to China. It has long been ranked as one of four major seafood items in China. Unfortunately, overfishing, pollution of the ocean environment, and other factors have led to a severe decline in the natural resources of large yellow croaker. Enhancement release of large yellow croaker has been conducted since 1987 and is considered an effective fishery management measure. Although the traditional tagged method can indirectly assess the effect of enhancement release, it has numerous disadvantages, such as high cost, complicated operation, tags easily falling off, and fish body damage, which obstruct the effectiveness of the assessment. Furthermore, few strategies and methods have previously been proposed to precisely assess the effect of enhancement release of large yellow croaker. Through mixing “labeled” individuals with a known parental origin and the released population at a certain proportion, andidentifying “labeled” individuals through parentage identification after recapturing, microsatellite marker technology calculates the rate of recapture with a higher precision, and is becoming more popular in the enhancement release assessment. To assess the applicability of microsatellite markers in evaluating the effect of enhancement releasing programs in Larimichthys crocea, this study used a total of 8 microsatellite loci with rich polymorphism to conduct parentage identification for 100 parents of released offspring and 295 individuals recaptured from Guanjingyang sea water. In addition, this study also proposed a method for evaluating the recapture effect of large yellow croaker enhancement programs based on microsatellite molecular markers. In total, 78 alleles were detected at the 8 microsatellite loci. The values of observed heterozygosity and excepted heterozygosity were 0.511–0.939 (mean 0.764) and 0.643–0.897 (mean 0.781), respectively, and the polymorphism information content of the 8 loci was 0.587–0.883 (mean value was 0.751). The results of simulated analysis using Cervus 3.0.7 software showed that the combined exclusion probability of individuals at the 8 microsatellite loci reached 99.99% or more with a confidence level greater than 95%. Among the 190 large yellow croakers recaptured from Guanjingyang sea water in July, only five were identified as the offspring of the 100 released parents, accounting for 2.63% of all recaptures. This study estimated that the proportion of the large yellow croaker from released individuals to the recaptured ones should be approximately 60.53% in July. The recapture rate of large yellow croaker released by Fufa company was around 0.0038% in July, while the marked individuals failed to be detected in the recaptured samples in August and September. The recapture rate of 0.0038% is lower than that of the traditional tagged release. Compared with traditional tags that have visible external-scale tags to assist with identification and recapture by fishermen, it was difficult to include the internal markers in the statistics, as the captured individuals were not detected by visual identification. Microsatellite markers can efficiently and “autonomously” implement numerous permanent carrying markers based on genetic characteristics, and will not damage the marked individuals. Therefore, the proportion of released individuals to recaptured samples, which was calculated through the microsatellite method, is closer to the real data as opposed to traditional tagged release calculations. All the marked individuals detected in this study were recaptured in water with a slow current on both sides of Guanjingyang, which further confirmed that Guanjingyang is a suitable feeding ground for large yellow croaker juveniles. Nevertheless, this study also found that no marked individuals were detected in August and September. This could be attributed to the small proportion of recaptured individuals and the wider range of release of the population at that time. This study provides a new method for assessing the effect of stock enhancement, and affirms that enhancement release can restore the wild stock of large yellow croaker to a certain extent.