16S amplicon hypervariable region V4 reads of specimens of encrusting coral bioeroding marine sponge Cliona varians in Neotropical Southern Caribbean Sea. The samples are of Colombian origin and they were obtained according to Amendment No. 5 to ARG Master Agreement No. 117 of May 26, 2015 granted by the Ministry of Environment and Sustainable Development -Colombia-. The conditions of use of this information by other research teams are CC BY 2.0 and other compatible NCBI, national and international regulations and agreements.