The genetic structure and genetic diversity in three natural populations of Neverita didyma were analyzed by using the molecular marker technique of inter simple sequence repeat (ISSR). The samples of the three populations were taken from the offshores of Dalian (DL), Yantai (YT) and Qingdao (QD), respectively. A total of 161 loci from 90 individuals were polymerase-chain-reaction (PCR) amplified with 13 primers. The proportion of polymorphic loci in the three populations ranged from 74.53 % to 85.09 %. The abundance of genetic diversity in the three populations arranged in a decent order was YT > QD > DL. The Nei′s gene diversity and Shannon′s information index of Neverita didyma was 03395 and 0.5113 at species level, 0.2811 and 0.4189 at population level, respectively, showing that the genetic diversity of Neverita didyma was relatively high. An analysis of the molecular variance (AMOVA) demonstrated that the among-population component accounted for 27.16 % of the total variation, while the within-population component accounted for 72.84 %. The within-population genetic variation was apparently larger than the among-population. The genetic differentiation coefficient (Gst), gene flow (Nm) and the average Nei′s genetic distance were 0.1720, 2.4063 and 01228, respectively among the three populations. The results indicate that although there is genetic differentiation of some extent among the three populations of Neverita didyma, such differentiation is well contained in the context of normal differentiation within the species. The results have laid the scientific basis for the conservation and utilization of the Neverita didyma resources.