Structural properties of the cordgrass, Spartina foliosa, were studied in parallel with nitrogen fixation rates and diversity of nitrogen-fixing microbes (diazotrophs) for two years in sediments of an early successional (6 year old) and a mature marsh at Tijuana Estuary (California, USA) via acetylene reduction and genetic fingerprinting (T-RFLP with nifH). Nitrogen fixation rates reflected biannual dynamics and differences in S. foliosa between marshes. In initial comparisons (fall 2005), S. foliosa height and aboveground biomass were less developed and average nitrogen fixation rates were higher in the early successional marsh than in its mature counterpart. By the following fall (2006), sediment organic content, nitrogen fixation rates and total rhizosphere diversity were similar between marshes, but S. foliosa aboveground biomass and porewater ammonium remained lower in the early successional marsh and diazotrophic community composition differed significantly. Diazotroph assemblages in surface sediments consistently differed from those in S. foliosa rhizospheres of the late-successional marsh, but not in the younger marsh, where rhizosphere diazotroph richness (T-RFs) declined from 2005 to 2006 in parallel with aboveground biomass of S. foliosa plants. These dynamics of diazotroph communities and S. foliosa suggest that ecological interactions of microbes and plants significantly influence wetland ecosystem function and succession.