Also known as South Seymour, Baltra is a small, flat island located near the center of the archipelago that was formed by a series of uplifts of submarine lava, resulting in flat plateaus. The island was of little interest to humans until the 1930s, when Franklin Delano Roosevelt visited aboard the USS Houston, as the US government sought to establish an air base in the Pacific to protect the western approach to the Panama Canal. While consideration was given to San Cristóbal because of its water supply and human population, Baltra was chosen because of its location at the center of the archipelago and its flat topography. Construction of the airbase began in February 1942 and within two months a mile-long airstrip was completed. With time, associated infrastructure grew to over 200 buildings, including barracks for 1,000 soldiers, hangars, office buildings, an outdoor beer garden, a cinema, and even a bowling alley (constructed after Eleanor Roosevelt visited the island and described conditions for the soldiers as “deplorable”). From the air it is still possible to see the foundation lines of many of these buildings. Soldiers stationed on Galapagos referred to Baltra as “The Rock” and were considered among the toughest members of the US Sixth Air Force.

At the end of the war, the United States turned the base over to the Ecuadorian government, which offered each head of household in Galapagos one of the buildings. Many carefully deconstructed their building to provide building material for their own homes on both Santa Cruz and San Cristóbal. Ecuador used the base to establish their own airstrip in Galapagos, with the first commercial flights arriving in 1963. Today the island continues to serve as an official Ecuadorian military base, with bases for both the Navy and the Air Force. Baltra has the primary fueling station for boats out of Santa Cruz.