Strong gradients in physico-chemical properties between abutting water masses create prominent transition zones in the marine environment. The Strait of Gibraltar forms the well defined boundary between the Mediterranean and Atlantic, and this paper examines spatial variation of hydroid assemblages in this transition zone. Although several studies highlighted the transitional character of the Strait and defined it as an ecotone, the benthic hydroid assemblages did not show differences between the Gulf of Cádiz and the Alboran Sea. However, there is an asymmetrical influence of the Atlantic waters on the coastal benthic ecosystems of the Alboran Sea, which maintains a more Mediterranean character in the hydroid assemblages of the northern coast, whereas a more Atlantic character was found in the rest of the studied sites. The transition zone between Atlantic and Mediterranean benthic communities could be associated with an Atlantic Influence Zone rather than with the Strait of Gibraltar itself.