Nibea albiflora is a commercially important marine fish species, which is widely distributed in Chinese, Japanese and Korean waters. Nibea albiflora has been intensively studied in China, including its basic biological characteristics and artificial reproduction. However, very few studies on N. albiflora were focused on genetic diversity, which has become an obstacle to further researches on the protection, management, rational exploitation and sustainable utilization of N. albiflora resources. The yield of N. albiflora has declined quickly due to increased efficiency of capture techniques and the leap of catch intensity. The information of genetic diversities of different populations will give us theoretical guidance in breeding and genetic improvement. In this study, a new molecular techonology, amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity and variation of two populations of N. albiflora from Qingdao and Xiamen sea areas. Procedures of AFLP analysis were essentially based on Vose et al. and Wang et al. A total of 47 individuals were studied using five primer combinations (E-AAC/M-CAG, E-AGG/M-CTT, E-AGG/M-CAG, E-AGC/M-CAT, E-AGC/M-CAG). AFLP bands were scored for presence (1) or absence (0) and transformed into 0/1 binary character matrix. AMOVA and mismatch distribution analysis were performed in Arlequin, Nei genetic diversity and Shannon genetic diversity index were calculated in POPGEN. A total of 461 loci ranging in size from 60 bp to 550 bp were detected from 47 individuals, of which 265 were polymorphic. The number of bands per primer combination varied from 66 to 126 and the percentage of polymorphic bands per primer combination ranged from 52.58% to 62.70%. The proportion of polymorphic loci, the Neigenetic diversity and Shannon genetic diversity index of Qingdao and Xiamen populations were 51.70% and 51.99%, 0.1022 and 0.0996, 0.1643 and 0.1622, respectively. The results showed that the genetic diversity of these two populations was at the same level. G_st value, Shannon genetic diversity index and AMOVA analysis indicated that the genetic variation mainly came from individuals within populations and there was no significant genetic differentiation between populations. The UPGMA tree based on AFLP data supported this result and no distinct clade was detectd. Mismatch distribution analysis and dominant gene frequency revealed that these two populations have the same genetic population structure. The results of AFLP analysis indicated that there is no significant genetic differentiation between two populations due to frequent gene flow. At present, the natural populations of marine fish, including N. albiflora, have been destroyed due to over exploitation and increasing marine pollution which caused the number of parent fish to be extremely diminished. These results provide information on the geneticst ructure of N. albiflora, which can be utilized to make informed mana gement decisions. However, AFLP markers are inherited as dominant markers, further studies utilizing codominant markers are needed for a better understanding of the genetic diversity of this fish.