Horizontal and vertical distribution of cephalopod paralarvae (PL) from the Mesoamerican Barrier Reef System (MBRS) in the Western Caribbean was studied during two oceanographic cruises in 2006 and 2007. A total of 1034 PL belonging to 12 families, 22 genera, 24 species, 5 morphotypes and a species complex were identified. Abralia redfieldi, Onychoteuthis banksii and Ornithoteuthis antillarum were the most abundant taxa. The taxonomic identification from these three species was corroborated with DNA barcoding (99.8–100% of similarity). Paralarvae of Octopus insularis were reported for the first time in the wild. Most PL occupied the Caribbean Surface Water mass in the 0–25 m depth stratum. Largest paralarval abundances were related to local oceanographic features favouring retention such as the Honduras Gyre and Cozumel eddy. No day-night differences were found in PL abundance, although Abralia redfieldi showed evidence of diel vertical migration. Distribution of PL in epipelagic waters of the MBRS was probably related to ontogenetic migration, hydrographic features of meso and subscale, and to the circulation regimes dominated by the Yucatan Current. The MBRS represents an important dispersion area for PL, potentially connecting a species-rich Caribbean community with the Gulf of Mexico and Florida waters.