In 1988 Panama designated 32,700 acres of Isla Bastimentos and its surrounding marine area as a national park. A corridor through the middle of the island forms a land bridge of some 4,100 acres between the windward and leeward coasts of the island. The largest portion of the park, approximately 28,600 acres, is marine habitat. The Zapatilla Cayes, also included in the park, are two beautiful uninhabited islands which make up part of the barrier reef which protects much of Isla Bastimentos.

The interior of the park is primary and secondary rainforest. Wildlife in the lowlands of Bocas del Toro includes species endemic to the region such as white-faced capuchins, night monkeys, two and three toed sloths, conejo pintado, margays, armadillos, exotic birds, bats, turtles, caimans, frogs, lizards, butterflies, and rare tropical insects. The park is also home to thousands of plant species including hardwoods, forest palms, vines, brophytes, ferns, bromeliads, orchids among others.

On the windward side of the park, the jungle canopy goes all the way to the edge of the beach. This area is a nesting site for four species of sea turtle. It includes a dramatic landscape with large rock faces, coves and inlets, spring fed creeks, offshore rock outcroppings and long stretches of beach. Ocean impact reef and deep ocean reef meet to form a dramatic underwater topography just offshore from the island. Rock chutes, crags, pinnacles and tunnels converge to make shelter for over 200 species of tropical fish. There are also many different formations of hard and soft coral.

The leeward side of Isla Bastimentos has coastal forest merging with lush tangled mangrove which plays an important role in the ecology of the nearby reef. Mangrove cayes dot the Bastimentos National Marine Park. Sea grass covers the shallow flats of white and pink coral sand. Both the health of the mangrove and the diverse coral reef is dependent upon the sea grass. Patch reefs of staghorn, brain coral and sponges provide a habitat for tropical fish, sea stars, sea cucumbers, crabs, conch, octopus and lobsters.