The recent expansion of the invasive lionfish throughout the Western Hemisphere is one of the most extensively studied aquatic invasions. Molecular studies have improved our understanding of larval dispersal, connectivity, and biogeographical barriers among lionfish populations, but none have included Mexican localities, an important area for the larval dispersal of Pterois volitans through the Western Caribbean and the Gulf of Mexico. Here, we present a genetic analysis of lionfishes collected along Mexican coasts, examining their connectivity with other Caribbean localities (Belize, Cuba, Puerto Rico) and the role of ocean currents on population structure. We collected 213 lionfish samples from seven locations comprising four countries. To evaluate genetic structure, mitochondrial control region and nuclear inter-simple sequence repeat markers were used. We found that lionfish collected along Mexican coasts show a similar haplotype composition (H02 followed by H01 and H04) to other Caribbean locations, and the H03 rare haplotype was not found. Haplotype composition in the southwest Gulf of Mexico suggests a discontinuity between the southern and northern areas of the Gulf of Mexico. The southern area clustered more strongly to the Caribbean region, and this is supported by the complexity of water circulation in the semi-enclosed region of the Gulf of Mexico. Mitochondrial genetic diversity parameters show small values, whereas nuclear markers produce medium to high values. Only nuclear markers highlighted significant genetic differentiation between the southwest Gulf of Mexico and Caribbean region, confirming a phylogeographic break between both regions. Separate analysis of Caribbean locations indicates restricted larval exchange between southern and northern regions of the Mesoamerican Barrier Reef System, potentially in response to regional oceanographic circulation.