The invasive Norway and black rats, introduced in the 17th century, feed on the eggs and hatchlings of the islands' native species, such as giant tortoises, lava lizards and iguanas.
Rats have also depleted plants on which native species feed and endangered bird species on the 19-island cluster 600 miles from Ecuador's coast.
"It's one of the worst problems the Galapagos have. (Rats) reproduce every three months and eat everything," said Juan Carlos Gonzalez, a specialist with the Nature Conservancy involved in the Phase II eradication operation on Pinzon island and the islet of Plaza Sur.
Phase I of the anti-rat campaign began in January 2011 on Rabida island and about a dozen islets.