Nitrogen fixing bacteria (diazotrophs) play a fundamental role in alleviating nitrogen limitation in oligotrophic oceanic waters. Recent evidence suggests that the marine waters of northern Australia are a potential hotspot of nitrogen fixation activity1, 2 , yet the microbial community underpinning this activity has not yet been explored. In addition, little information exists regarding spatiotemporal patterns in the identity and activity of diazotrophs within the largely oligotrophic oceanographic provinces surrounding Australia. We aimed to address this gap by characterising diazotrophic phylotypes and estimating nitrogen fixation in the tropical north, subtropical/temperate south-east and within a temperate, inverse estuary in South Australia. Pyrosequencing of the nifH gene was used to investigate the phylogeny and relative proportion of diazotrophic groups. Discrete N fixing assemblages were observed within the tropical and temperate provinces, driven by differences in the composition of the diazotroph community. Pronounced shifts from Trichodesmium dominated assemblages in the shallow seas of tropical northern Australia to Candidatus Atelocyanobacterium thalassa (UCYN-A) and gammaproteobacteria dominated communities in temperate systems were observed. Substantial differences in diazotroph community composition and nitrogen fixation activity, measured using the 15N-N2 stable isotope tracer approach, were observed over seasons within tropical and subtropical sampling regions. Rates of nitrogen fixation were found to be generally higher in shallow tropical waters, and within these regions were higher in winter than in spring. Network analysis revealed that physical properties of the water column, including temperature, salinity and bottom depth, are strongly correlated with globally important diazotrophic phylotypes such as Trichodesmium and UCYN-A. Our findings support the hypothesis that Australian marine waters provide a hotspot of nitrogen fixation, harbouring globally significant and highly active diazotroph assemblages which are dynamic across spatial and temporal scales.