Title: Paired Environmental DNA (eDNA) and Environmental RNA (eRNA) Metabarcoding Survey of Tropical Marine Habitats Around San Andrés Island, Colombia Description This dataset contains raw amplicon sequencing data (FASTQ files) and processed operational taxonomic unit (OTU) tables generated from paired environmental DNA (eDNA) and environmental RNA (eRNA) samples collected from marine habitats surrounding San Andrés Island, Colombia, within the Seaflower Biosphere Reserve. Sampling was conducted at 19 sites representing a range of tropical marine environments, including coral reefs, mangroves, a seagrass meadow, shipwrecks, a cenote, and coastal infrastructure. At each location, paired eDNA and eRNA water samples were collected to compare biodiversity signals recovered from environmental DNA and environmental RNA templates. Amplicon sequencing targeted the cytochrome oxidase I (COI) region and was performed by NatureMetrics. Bioinformatic processing yielded 1,944 operational taxonomic units (OTUs) spanning diverse marine eukaryotes, including animals, algae, fungi, and protists. Of these OTUs, 1,015 were detected by both molecular approaches, 305 were unique to eDNA, and 624 were unique to eRNA. The dataset was generated to evaluate the extent to which eRNA provides complementary biodiversity information relative to eDNA and to assess whether eRNA is biased toward metabolically active organisms in natural marine ecosystems. The study represents one of the first ecosystem-scale field comparisons of paired eDNA and eRNA metabarcoding across multiple habitat types within a tropical marine seascape. Files included: • Raw demultiplexed sequencing reads (FASTQ format)• Sample metadata describing site identity, habitat type, and molecular template (eDNA or eRNA)• OTU abundance tables• Taxonomic assignment tables• Associated analytical outputs used in biodiversity and community composition analyses Sampling locations encompass coral reef, mangrove, seagrass, shipwreck, cenote, and anthropogenic marine habitats around San Andrés Island, Colombian Caribbean Sea. Keywords: environmental DNA, eDNA, environmental RNA, eRNA, metabarcoding, biodiversity monitoring, tropical marine ecosystems, coral reef, seagrass, mangrove, COI, operational taxonomic units, protists, marine ecology, Seaflower Biosphere Reserve, San Andrés Island, Colombia.