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Avifauna are essential for maintaining the structure and functioning of mangrove ecosystems, which are particularly sensitive to habitat transformation. Although exotic cordgrass, Spartina alterniflora, is an increasing threat to mangrove ecosystems (including the associated unvegetated shoals) of China, its effects on the avifauna in such ecosystems are poorly understood. In Zhanjiang, China, the avifaunal Shannon-Weiner diversity, Simpson's diversity, Margalef's species richness, Pielou's evenness and density indices were compared in (1) an Avicennia marina monoculture vs. an S. alterniflora-invaded A. marina stand (a mixture of A. marina and S. alterniflora) and (2) an unvegetated shoal vs. an S. alterniflora-invaded shoal that had rapidly become an S. alterniflora monoculture. All avifaunal community parameters except for the Simpson index were significantly lower in the S. alterniflora thorn A. marina mixture than in the A. marina monoculture, and in the S. alterniflora monoculture than in the unvegetated shoal. These results indicate that the presence of S. alterniflora reduces the suitability of the Zhanjiang mangrove ecosystem for avifauna. Among the four habitats, the Shannon-Weiner diversity index, species richness, and density of the avifaunal community were highest in the unvegetated shoal. Further analysis indicated that the differences in the avifaunal community between invaded and noninvaded sites were associated with vegetation characteristics (mainly plant height and density) and macrobenthic faunal metrics (mainly species richness and density). The reduced avifaunal diversity and abundance associated with S. alterniflora invasion probably resulted from the decline in food resources or from the increased difficulty in foraging and roosting. The findings indicate that the conservation of birds in mangrove ecosystems may depend on controlling or eradicating exotic S. alterniflora, maintaining tidal mudflats, and diversifying the habitats in mangrove wetlands.