In the present study, random amplified polymorphic DNA (RAPD) molecular marker was used to study the population genetic diversity and structure of five Zostera marina L. populations distributed in Shandong Peninsula: Laizhou bay, Xiaoshi Island, Li Island, Chu Island and Huiquan Bay. Based on the obtained results, suggestions for Z. marina population protection and for seaweed meadow restoration in Shandong peninsula were put forward. In the experiment, 42 bands were obtained by RAPD markers amplified through 10 selected primers. The percentage of polymorphic bands was 92.86%. The results showed that the populations in Shandong Peninsula had high genetic diversity and high genetic differentiation. The AMOVA demonstrated that the inter population component accounted for 99.68% of the total variation, while the intra population component accounted for 0.32%. Mantel tests showed that 5 populations of Z. marina L. had no correlation between genetic distance and geographic distance. The population in Laizhou Bay that showed the lowest genetic diversity should be given priority protection. The populations in Li Island and Huiquan Bay that showed highest genetic diversity can be used as the first choice for seaweed meadow transplanting restoration in Shandong Peninsula.