Salt marsh habitats in estuaries play important roles in species compositions and macrobenthos abundances. Here, the macrobenthic communities and environmental conditions in two habitats, which are dominated by the invasive species Spartina alterniflora (SA) and native species Suaeda glauca (SG), in the Yellow River Delta were studied to assess habitat function. The seasonal data showed that the species diversity and abundance of macrobenthos in the SA habitat were much higher than those in the SG habitat. The functional groups in the former showed significant seasonal changes and shifted from polychaeta (68%) in spring to mollusca (97%) in autumn, but in the latter, it was dominated by crustacea (63-86%), mollusca (1-25%) and polychaeta (9-13%), and only mollusca exhibited obvious seasonal changes. The sediments in the SA habitat contained richer organic matter contents and exhibited higher Chl- a concentrations than those in the SG habitat, although the grain sizes were coarser in the SA habitat. At the seasonal scale, macrobenthos in the SA habitat displayed significant negative correlations with salinity and organic matter. The results indicated that the macrobenthos functional groups in the SA habitat were simpler and more sensitive to environmental changes than those in the SG habitat. The vegetation structures may give rise to the differences in macrobenthos distributions in both habitats, which need to be further observed and explored.