In order to study the structural characteristics of the epiphytic algal community of eelgrass (Zostera marina) along Shandong Peninsula, we conducted investigations at Zhanqiao, Qingdao, Shuangdao Bay, Weihai, and Moon Lake, Rongcheng in March (spring), June (summer), September (autumn) and December (winter) 2012. Epiphytic algal communities of eelgrass in different seasons were comparatively analyzed regarding its diversity index and evenness index using cluster analysis and multidimensional scaling analysis (MDS). In total, 17 species were identified, belonging to 3 classes and 14 genera. Among them, there were 4 genera and 5 species of Rhodophyceae, 4 genera and 4 species of Phaeophyceae, and 6 genera and 8 species of Chlorophyceae. The greatest number of species (7) was found at Zhanqiao and Shuangdao in spring, and the lowest (1) at Moon Lake in both autumn and winter. The greatest biomass was found in spring, and the lowest in autumn (Zhanqiao), winter (Shuangdao) and summer (Moon Lake). The Shannon diversity index and Pielou’s evenness index were the lowest at Zhanqiao, while the diversity index was the highest at Shuangdao. The species diversity index and evenness index at the six locations were highest in summer, and lowest in winter. The epiphytic algal community structure varied significantly between at the different locations and at most of the different sampling sites of same locations in different seasons, indicating that seasonal variations and geographical differences played important roles in the variations of community structure.