Nine individual adult polyps were sampled off Vulcano Island, Italy, from a natural CO2 gradient of decreasing pH nearby a volcanic vent. Three different sampling locations were chosen for this study, representing seawater pH conditions 8.2, 7.9, and 7.6. Total RNAs from three different tissues of the nine polyps (mouth piece, tentacles and body wall), corresponding to three biological replicates at each location, were isolated. RNAs isolated from the three different tissue samples of each specimen were pooled together in equal amounts before proceeding with small RNA enrichment, library preparations and sequencing using SOLiD 5500xl platform. Libraries were barcoded and were sequenced on three lanes of a slide, yielding 142 million reads. Small RNA sequences coming from one individual from the same sequencing library were pooled together. In addition, DNA from one individual of A. viridis (pH 8.2) was sequenced using Illumina HiSeq 2500 platform, yielding 144 million paired-end reads.