The diversity of shipwrecks cyanobacteria in shallow water of New Calabar River, in River State -Nigeria was examined. Bio-concretions from three shipwrecks located at the estuary of New Calabar River were collected and the visual examination of the bioconcretions revealed 3 types of rusticles: Brown rusticles (braided structures attached on the wreck surfaces), Dendritic concretion (layered coatings of different concretions) and Biofilm (slimy coatings). The 16S rRNA gene sequences from the rusticles was performed by Next Generation Sequencing Technique to determine the nucleotide sequence of cyanobacteria present in the rusticle samples using automated Illumina Miseq analyser. The results revealed a diversity of cyanobacteria in the rusticle samples. The cyanobacteria composition showed different species of diazotrophic filamentous genus Trichodesmium., it dominated the bio-concretion, having in abundance 4 of its species; T. erythraeum (8.75%), T. hildebrandtii (1.08%), T. contortum (1.04%) and T. tenue (1.02%). The availability of iron on the bio-concretions could explain the reason for the presence of the Trichodesmium clades present. Phormidiaceae, cyanobacteriacea, we can associate the formation of rusticles by cyanobacteria as one of their eroding characteristics on shipwrecks. This study attempts to validate the role of mat-matrix forming cyanobacteria in aerobic corrosion in shallow water shipwrecks.