San Jose, the second largest island at 44 sq. kilometers and a 2 hour boat ride or a mere 20 minute plane trip from Panama City, boasts perhaps the best opportunities for fishing, diving, and general wildlife observation. The waters surrounding the irregular shoreline are considered some of the world's best deep sea fishing grounds. For the fisherman, there are tuna, dolphin, marlin, and red snapper as well as giant oysters, lobster, shrimp and marine turtles to wonder over. Isla del Rel is the largest island of the chain, larger than the other islands combined. The waters surrounding this island teem with whales, dolphins, sea turtles and game fish. Contadora, a resort island complete with a large hotel and cabins, has a dozen beaches around its perimeter from which diving and snorkeling is a favorite sport. High and low tide may differ by 17 feet, however, so perhaps the diver's best snorkeling experience remains at low tide. An array of stony corals resemble the reefs found in the distant South Pacific Islands. While perhaps less comfortable for divers, sharks may be encountered and observed, especially between Playas Sueca and Larga beaches.

Named Islas de las Perlas by the Spanish explorer Balboa after encountering natives whom he said paddled with oars encrusted with pearls, the island chain was claimed in Spain's name and proceeded to become a veritable favorite for pirates. Unfortunately, the natives did not enjoy the company; as most fell ill to the European diseases and died in some of the Spanish conquests. They were replaced by African slaves whose descendants live on the islands today. Surprisingly, given its 200 year history as a haunt for pirates, there are few known wrecks in the Pearl Islands. The most famous may be the San Jose, a Spanish galleon, believed to be off the island San Jose, but it was not been recovered.

For those less fish-inclined, the wildlife on San Jose Island includes wild pigs, agoutis, giant pigeons, deer, and over 100 species of birds. Punta Chame, surrounded by the sea and pearly white sands on both sides, is the perfect destination for wind sailors and kiters. For the avid bird watcher, a must-stop is Isla Pacheca, located in the northern end of the island chain. The island claims thousands of Frigate birds, boobies, cormorants, terns, egrets, pelicans and herons.