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San Ignacio, Baja California Sur. San Ignacio is a palm oasis town in MulegÃ© Municipality of northern Baja California Sur state in Mexico. It is located on Mexican Federal Highway 1 between Guerrero Negro and Santa RosalÃ­a.
1 Close encounters with the friendly gray whale cows and calves in San Ignacio Lagoon, a UNESCO World Heritage Site. 2  Opportunities to see blue, fin, humpback, Bryde's, sperm, and killer whales in the Sea of Cortez, plus snorkeling with tropical fish.uring the Loreto / Sea of Cortez portion of the trip, we stay in comfortable hotels and enjoy meals in local restaurants. In San Ignacio Lagoon we stay in a catered camp situated on the water's edge, with safari-style tents that have solar-powered lights and platform beds.