Abstract: With data for distributions and diversities of macroinvertebrates from 12 main subtidal zones in the bays of Fujian on August 2010, we investigated species composition, biodiversity and community structure, as well as their relationships with environmental factors. The results showed that 382 macroinvertebrates were recorded, which included 170 annelids, 75 crustaceans, 78 mollusks, 19 echinodermata, and 40 other species. The species richness, individual abundance, biomass and biodiversity indices showed significantly spatial variability. The average of species richness was (55±21), with the highest (92) in Luoyuan Bay and the lowest species (25) in Jiuzhen Bay. Polychaetes was dominant species in each bay, with an average percentage of (51.8±5.5)%. Zhaoan Bay had the highest average individual abundance with (1330±1094) ind·m^-2, followed by Fuqing Bay, Xiamen Bay and Meizhou Bay, while Quanzhou bay had the lowest. Xinghua Bay had the highest average biomass with (821.2±2387.7) g·m^-2, followed by Fuqing Bay and Xiamen Bay. Both richness index and Shannon diversity were much higher in Luoyuan Bay, Meizhou Bay, Shenhu Bay, Xiamen Bay and Dongshan Bay, and their values were low in Fuqing Bay and Jiuzhen Bay. The mean value for d and H across all bays was (0.80±0.09) and (2.73±0.64), respectively. The macroinvertebrates of the study area were divided into 14 groups using a criterion of 20% similarity. The stations in Luoyuan Bay had the highest similarity and the lowest spatial variability, and followed by Sansha Bay, Fuqing Bay, Shenhu Bay and Zhaoan Bay. The higher variability of community composition was found among the stations for the rest bays. On the basis of Spearman correlations among species richness, biodiversity indices and environmental factors, as well as PCA analy-sis, Cu in the sediment, water depth, and dissolved inorganic phosphorus in bottom water were the main factors driving the spatial variability of composition and distribution of macroinvertebrates in the study area.