In order to explore the seasonal variation of the eco-groups in the coastal waters of central Fujian Province, we conducted three comprehensive marine surveys during December 2009 and April and August 2010, and the species composition and eco-groups were discussed by using non-metric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM). The results showed that a total of 40 species was identified in winter, warm-water-species were the dominate eco-groups. But the ratio of warm-temperature-species were the highest (30%) among three seasons, and accounting for 17.65% and 16.96% of the biomass and individual density respectively. There were 39 species of fish in spring, and eco-groups are still dominated by warm-water-species. The biomass and individual density of the warm-water-species accounted for 86.48% and 94.52% of the total amount respectively. In summer, fish species accounted for 61, and warm-water-species appeared in large number by 55 species, accounting for 97.17% and 99.35% of the biomass and individual density respectively. Affected by Zhejiang-Fujian coastal water and Taiwan Strait warm current water alternately, species turnover rate and the number and density of warm water species were increased gradually, and accompanied by the estuarine species replaced by coastal species from winter to summer. The phenomenon was related to fish spawning, feeding and wintering migration, when Zhejiang-Fujian coastal water and Taiwan Strait warm current water occupied this area. It is concluded that the seasonal variation of eco-groups and species compositions in the coastal waters of central Fujian Province may be affected by the changes of water masses.