Bromeliads tank water or phytotelma is an eutrophic microenvironment where microorganisms have evolved to resist sudden changes in pH and nutritional competition. Metagenomics studies have been poorly studied in bromeliads and environmental DNA (eDNA) characterization for its microenvironment is deficient in Puerto Rico. Therefore, the data represents the microbial communities inhabiting bromeliads phytotelma. eDNA was extracted using Metagenomic DNA Isolation Kit for Water. Next-Generation-Sequencing technology (Illumina MiSeq) was used for sequencing the isolated eDNA. This data provides an insight about diversity and functional depiction of microorganisms inhabiting bromeliads phytotelma. The data of this metagenome is available in the BioSample Submission Portal as Bioproject PRJNA39461 and Sequence Read Archive (SRA) accession number SRP114300. MG-RAST metagenomic analysis server is located under the study ID mgp79812.