Bycatch represents a conservation problem when endangered species are affected. Sea turtles are highly vulnerable to this threat as their critical habitats overlap with fishing zones in all regions of the world. We used sequences of the mitochondrial DNA control region obtained from loggerhead (Caretta caretta) and green (Chelonia mydas) turtles to determine the migratory routes between nesting habitats in the Yucatán Peninsula and their critical marine habitats in the Northwest Atlantic. Mixed Stock Analysis revealed that loggerheads from Quintana Roo migrated to foraging areas in the northwestern Atlantic. Migratory routes used by green turtles are determined by their natal nesting colony: (1) green turtles from the Gulf of Mexico migrate to foraging aggregations in Texas and the northern Gulf of Mexico, (2) Mexican Caribbean turtles travel to foraging grounds in Florida, and (3) a smaller proportion of individuals born in the Yucatán Peninsula display a local connectivity pattern. Our results suggest that the migratory corridors used by Mexican loggerheads overlap with longline fisheries in the mid-Atlantic where sea turtle bycatch is comprised predominantly of immature individuals. Green turtles from the Yucatán Peninsula migrate to critical habitats that overlap with shrimp trawl fisheries within the Gulf of Mexico. Bycatch data and the identification of migratory corridors used by loggerheads and green turtles suggests that shrimp trawl fisheries on the east coast of the U.S. and the Gulf of Mexico pose a serious threat to the conservation and recovery of Mexican sea turtle populations.