Macro-algae flora of the mussel culture zones in Gouqi island, Zhejiang Province, was surveyed from 2014 to 2015. Seventy species of macro-algae were identified, belonging to 31 genera, 21 families, 14 orders, and three phyla. Thirty-eight species from 16 genera belong to Rhodophyta, 21 species from seven genera belong to Phaeophyta, and 11 species from eight genera belong to Chlorophyta. Rhodophyta, Chlorophyta, and Phaeophyta contributed to 54.29%, 30%, and 15.71% of the total number of species, respectively. The dominant species were Undaria pinnatifida, Sargassum horneri, Grateloupia livida, Grateloupia turuturu, Ulva pertusa, Ulva lactuca, Hypnea boergesenii, Ulva linza, Cladophora utriculosa, and Amphiroa ephedraea. Seasonal alternation of macro-algae species was evident; there were 52 species in spring, 42 species in winter, 38 species in autumn, and 30 species in summer. Macro-algae biomass was highest in spring and lower in autumn > summer > and winter. The diversity of macro-algae communities also changed seasonally; the diversity index (H’) was highest in autumn and lower in summer > winter > and spring. The results of de-trended correspondence analysis suggested that temperature was the most important environmental factor affecting the distribution of the macro-algae in mussel culture zones. Wind, water currents, and human disturbances were also important factors affecting algal communities.