Samples were collected in order to document the bacterial ribotype (16S rRNA gene) diversity associated with the SML of healthy Montastraea faveolata and Porites astreoides corals at three sites across the Caribbean in: the Florida Keys, St. Thomas, U.S.V.I., and Belize. The bacterial assemblages associated with the SML of these colonies (n = 12) were analyzed using 454 barcoded-pyrosequencing of 16S rRNA gene amplicons. Samples were amplified using the bacterial forward primer 347F, which included the primer B adaptor for pyrosequencing and the unique 10 bp MID-barcode on the 5-prime end (5'-CGTATCGCCTCCCTCGCGCCATCAG-MID-GGAGGCAGCAGTRRGGAAT-3'), in addition to the bacterial reverse primer 803R (5'-CTACCRGGGTATCTAATCC-3').