The star barnacle, Chthamalus stellatus Poli, populates the Mediterranean Sea, the North-Eastern Atlantic coasts, and the offshore Eastern Atlantic islands. Previous studies have found apparent genetic differences between the Atlantic and the Mediterranean populations of C. stellatus, suggesting possible geological and oceanographic explanations for these differences. We have studied the genetic diversity of 14 populations spanning from the Eastern Atlantic to the Eastern Mediterranean, using 63 genomic polymorphic sites. We have found that these populations form four distinct clusters: Eastern Atlantic, Western Mediterranean, Mid-Mediterranean and Eastern Mediterranean, with evident connectivity between them. We examined here environmental conditions like surface currents, water salinity and temperature as probable factors that have formed the population structure. We suggest that C. stellatus is a suitable marine animal for studying how geological events and hydrographic conditions shape the fauna in the Mediterranean Sea.