This study focuses on the macrobenthic community of an unvegetated mudflat and that of a Schoenoplectus triqueter (synonym: Scirpus triqueter) marsh in the Southern Bank of the Hangzhou Bay, China. Samples were collected between April 2010 and January 2011 in order to evaluate possible effects of seasonality on the species composition for each habitat. Twenty-three species were found in each habitat, with higher crustacean and insect richness in the vegetated area, compared to a higher number of polychaete and mollusc species observed in the mudflat area. The highest macrofaunal abundance was recorded in summer whilst the lowest was registered in autumn. Heteromastus filiformis and Laternula marilina were the main contributors to the high abundance in the Hangzhou Bay. The results show higher mean macrobenthic abundances in the S. triqueter marsh (1,707 ind/m2 ± 1,669 SD) compared to that of the mudflat area (1,172 ind/m2 ± 1,115 SD). However, the highest mean biomass was found in the mudflat habitat (0.73 g/m2 ± 0.84 SD as opposed to 0.64 g/m2 ± 0.59 SD from the S. triqueter marsh) indicating the occurrence of larger specimens. Multivariate analyses indicate significant differences in the species composition between both habitats, confirming the importance of habitat structure on macrofaunal assemblages.