To test whether invasive Spartina alterniflora marshes were functionally equivalent to native Scirpus mariqueter marshes, the present study used bottomless lift nets (20 m2) during 12 high-tide events from August to October 2008 to compare nekton densities and biomass between the two marsh types in the Dongtan wetland. A total of eight species of fish, two species of shrimp, and three species of crab were collected. So-iny mullet Chelon haematocheilus, keeled mullet Liza carinata, Asian freshwater goby Acanthogobius ommaturus, and ridge-tail prawn Exopalaemon carinicauda dominated samples from the two marsh types and accounted for over 90% of the total catch. There were significantly greater densities and biomass (p < 0.05) of total nekton (all species combined) and two mullets (C. haematocheilus and L. carinata) in S. alterniflora marshes than in S. mariqueter marshes in August 2008, while no significant differences (p > 0.05) between the two marsh types were observed for densities and biomass of any species or total nekton in September and October 2008. Non-metric multidimensional scaling ordination did not show clear separation of samples between the two marsh types (r = 0.071, p = 0.159). Furthermore, there were no habitat-specific differences (p > 0.05) in the size distributions of the three numerically dominant species (C. haematocheilus, L. carinata, and A. ommaturus). We concluded that S. alterniflora marshes were utilized by nekton in a fashion similar to their utilization of native S. mariqueter marshes under similar physical conditions.