The Bahía Magdalena lagoon complex (BMLC) is an extremely productive and biologically diverse embayment on the Pacific coast of Baja California Sur, Mexico, and one of the most important fishing ports in the state. Local hydrologic conditions are largely determined by the differential influence of the California Current and California Countercurrent, with upwelling also affecting the physical characteristics of west–central Bahía Magdalena. Because of its subtropical location and variable hydrology, the BMLC is considered a transitional zone between temperate and tropical faunal regions. Tropical species are dominant among most taxa, especially in Bahía Almejas, but species composition is highly variable and coupled with environmental conditions.