This study was conducted to compare the microbial diversity and composition between the more protected reefs in Jardines de la Reina (Gardens of the Queen), Cuba and the more impacted reef-systems of Los Canarreos, Cuba and the Florida Keys, U.S.A. Seawater samples were generated by filtering 2 L of seawater onto filters, extracting the DNA, amplifying the V4 hypervariable region of the 16S ribosomal RNA gene, and constructing and sequencing the MiSeq library. The raw sequence reads are uploaded here. Reef depth seawater DNA was also harvested from select reef locations in Jardines de la Reina and the Florida Keys and sequenced with shotgun metagenomic sequencing.