The genetic diversity of Trichodesmium, a marine nitrogen-fixing non-heterocystous cyanobacterium of great ecological importance, was examined using the partial gene sequences of the small subunit ribosomal RNA (16S rDNA) gene and the regulatory gene hetR. Different species and morphotypes (fusiform and spherical colonies) of Trichodesmium were collected in the northern Caribbean Sea, the central Atlantic Ocean and southern Pacific Ocean. The trichome morphologies were observed with light microscopy before DNA extraction and PCR amplification. Phylogenetic analysis of 16S rDNA revealed that all cyanobacterial sequences from the colonies of Trichodesmium spp. were very closely related to the laboratory culture of Trichodesmium sp. NIBB 1067. The overall results from the hetR analysis were congruent with that of 16S rDNA, but the variation in nucleotide sequence between different species was higher within the hetR gene. The sequence data showed that three main clades were represented. One clade comprised sequences from Trichodesmium hildebrandtii Gomont and Trichodesmium thiebautii Gomont (including both its fusiform and spherical colony forms). Sequences from Trichodesmium contortum Wille and Trichodesmium tenue Wille constituted a second clade. The third clade contained Trichodesmium erythraeum Ehrenberg together with the two laboratory strains of this species, Trichodesmium sp. NIBB 1067 and Trichodesmium sp. IMS 101.