Efforts to define the marine connectivity among populations have been focused overwhelmingly on corals, sponges and fish populations, but are lacking in other well represented marine taxa. The sea urchin Echinometra lucunter lucunter was selected due to its wide distribution throughout the Caribbean Sea and its biological and ecological characteristics. The aim of this research was to postulate genetic connections between populations of Echinometra lucunter lucunter throughout the Caribbean Sea to detect whether the marine discontinuities identified for other taxa affect their connectivity, a critical issue for future conservation and management. Specific microsatellites were used to detect the genetic structure of E. lucunter lucunter through the region. The results showed clear evidence of genetic structure and gene flow through the Caribbean region, with three genetic populations from the south-west to the north-east: first the Colombian Caribbean Sea, a second population related to Venezuela and Belize, and a third group defined for Puerto Rico in the North-East. The evidence of structure and gene flow between the populations of E. lucunter lucunter is related to marine discontinuities such as the influence of physical factors (continental margin, Caribbean currents, calcareous rock as the main substrate, riverine discharges) and their variation through the area, as well the biological characteristics of the specie (e.g., assortative mating through gamete recognition, stochastic reproduction, patchy gamete distribution). These results will facilitate their conservation efforts in the area and offer important key data for the application of conservation and management strategies of Marine Protected Areas