<p>Diversity and community composition of nitrogen fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of <i>nifH</i> clone libraries. Representatives of the all four main clusters of <i>nifH</i> genes were detected. Cluster I sequences were most diverse in the surface waters and the most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. Cluster II, III, IV assemblages were most diverse at oxygen depleted depths and none of the sequences were closely related to sequences from cultivated organisms. The OTUs were biogeographically distinct for the most part – there was little overlap among regions, between depths or between cDNA and DNA. Only a few cyanobacterial sequences were detected. The prevalence and diversity of microbes that harbour <i>nifH</i> genes in the OMZ regions, where low rates of N fixation are reported, remains an enigma.</p>