Denaturing gradient gel electrophoresis (DGGE) was employed to resolve PCR-amplified nifH sequences from vegetated and unvegetated sediments from two oligotrophic seagrass bed sites on San Salvador Island, Bahamas, in order to assess diazotroph species composition. All DGGE profiles from these sites showed the same prominent bands. These bands were sequenced, yielding 67 different nifH sequences, which were used in phylogenetic reconstructions. Most sequences were from anaerobes, but some were affiliated with the alpha- and (gamma-+beta-) Proteobacteria. Several NifH sequences were nearly identical to those from Azospirillum brasilense and Vibrio diazotrophicus. These seagrass bed sediments support a diverse diazotroph assemblage that is, at least superficially, similar to that associated with an intertidal grass (Spartina alterniflora).