Decapterus maruadsi in Fujian coastal waters has been facing considerable fishing pressure because the resources of main economic demersal fishes have been exhausted. The information of stock structure of different populations will give us theoretical guidance in planning management and conservation of natural resources and in genetic improvement programs. In this study, amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity and variation of two populations of D. maruadsi from Eastern and southern Fujian coastal water. 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 conducted in POPGEN, genetic distance between individuals were computed in Phyltools and the UPGMA tree was generated in MEGA. A total of 563 loci ranging in size from 100 bp to 450 bp were detected from 62 individuals using eight primer combinations, of which 364 were polymorphic. The number of bands per primer combination varied from 54 to 84 and the polymorphic bands per primer combination ranged from 45.83% to 84.44%. The proportion of polymorphic loci, the Nei genetic diversity and Shannon genetic diversity index of these two populations were 62.70 % and 58.97 %, 0.187 5 and 0.180 9, 0.287 8 and 0.2763, respectively, revealing no significant difference (P>0.05) between the two populations. The results showed that the genetic diversity of these two seemed at the same level. Compared with other fishes, the genetic diversity of D. maruadsi in the coastal waters of Fujian province is above the middle level, with a higher genetic diversity, indicated that the population genetic structure of D. maruadsi had not been destroyed. Wide range of habitats, unbiased sex ratio and the characteristics of its distribution could be the reasons for the higher genetic diversity. G_st value, Shannon genetic diversity index and AMOVA analysis indicated that the genetic variation mainly came from individuals within populations. The UPGMA tree based on genetic distance between individuals exhibited no correlation between clades and geographic distribution. N_mshowed that there was frequent gene flow between the two populations. 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. Therefore, it draws a conclusion that D. maruadsi in the costal waters of Fujian province can be assigned to the same management unit. Annual migrations and larval drift in the ocean currents could be the reasons for little genetic structure in the studied area. However, AFLP markers are inherited as dominant markers, further studies utilizing codominant markers are needed for a better understanding of the genetic diversity of this fish.