Like their freshwater analogues, marine cyanobacteria represent a potential risk to human health as they can produce an extensive array of toxins. Blooms of potentially toxic marine cyanobacteria are predicted to increase in frequency and extend with climate change and eutrophication, especially in tropical lagoons. Cyanobacterial mats also harbour many species of bacteria and eukaryotic organisms, some of which have also been linked to human poisonings after consumption of contaminated fish or molluscs. In the present study we used 16S and 18S ribosomal RNA gene metabarcoding to characterize the taxonomic diversity of 66 benthic cyanobacterial mats collected from six islands in three different countries of the South Pacific: Kingdom of Tonga, Cook Islands and French Polynesia. There was a significant difference in cyanobacterial communities among islands with 30 genera recorded. Although the core bacteria remained constant among mats, there were significant differences both within and between islands in their community structure, even when the mats were dominated by the same cyanobacteria genera. Eight potentially toxic genera of dinoflagellates co-occurred in the mats of benthic cyanobacteria, indicating that more studies are needed given the occurrence of potentially toxic taxa.