The Galapagos National Park said La Cumbre volcano began spewing lava, gas and smoke and steam on uninhabited Fernandina Island on Saturday after four years of inactivity.
Following a flight over the island, Galapagos National Park official Oscar Carvajal said, "We saw a crack 200 meters long from which lava is coming out."
Carvajal said rivers of lava were also sighted moving to other points of the island.
The park said in a statement that the eruption is not a threat to people living on nearby Isabela Island, but lava flowing to the sea is likely to affect marine and terrestrial iguanas and other fauna.
A park official told AP Television that it was hoped the heat from the eruption would alert the maritime iguanas and the birds and instinct would force them to leave.
There are around 700,000 maritime iguanas at Galapagos National Park, a colony of 300 live in Fernandina island.
The Galapagos are home to unique animal and plant species that became the basis for much of Charles Darwin's theory of evolution.
Scientists say Fernandina, with 250 square miles, is the island with the most volcanic activity in the archipelago but other islands have also seen eruptions in recent decades.
La Cumbre, 4,842 feet, last erupted in May 2005.