The name likely comes from the Spanish word yunque, meaning anvil, a reference to the flat-topped profile of the Sierra de Luquillo range when viewed from the north. But the Spanish may have borrowed from something older. The Taino people, who carved petroglyphs into the riverbed boulders that still survive here, called the mountain Yukiyu, after the spirit deity Yokahu. Whether anvil or god, the name suits a place where clouds settle onto the peaks and refuse to leave. El Toro, the highest summit, reaches 3,494 feet above sea level. Some areas receive over 240 inches of rain per year. That relentless moisture sustains four distinct forest types stacked by elevation: tabonuco forest in the lowlands gives way to palo colorado, then sierra palm, and finally elfin woodland near the summits, where gnarled, moss-draped trees grow no higher than a person.

The Spanish arrived on the island of Borinquen in 1493, and by 1509 they had found gold in the Fajardo and Blanco rivers that drain these mountains. Mines opened along the Sabana, Prieto, La Mina, Mameyes, and Espiritu Santo rivers. But the forest itself they largely left alone. No evidence of permanent Taino settlement has been found within its boundaries either, suggesting the indigenous people considered it sacred ground. In 1876, King Alfonso XII of Spain proclaimed the forest a Crown Reserve, making it one of the earliest protected forests in the Western Hemisphere. When the United States took control of Puerto Rico in 1898, President Theodore Roosevelt established it as the Luquillo Forest Reserve in 1903. That early protection may explain why El Yunque still harbors species found nowhere else on Earth.

The Puerto Rican parrot once numbered in the hundreds of thousands across the island. By 1975, only 13 remained in the wild, all of them in El Yunque. Habitat loss, hunting, and nest predation by rats and pearly-eyed thrashers had driven the species to the edge of extinction. Recovery efforts began with captive breeding programs and the installation of artificial nest boxes to replace the large tree cavities the parrots require. Progress has been painfully slow. Hurricane Hugo in 1989 halved the wild population. Hurricane Maria in 2017 devastated the forest canopy, stripping leaves and snapping trunks across thousands of acres. Yet the parrots persist. The Puerto Rican broad-winged hawk, the sharp-shinned hawk, and the elfin woods warbler also depend on this forest, making El Yunque one of the most critical conservation sites in the Caribbean.

Of the roughly 16 species of coqui known in Puerto Rico, 13 live in El Yunque. The most famous, Eleutherodactylus coqui, produces its two-note call beginning at sunset and continuing until dawn. The first note, the "co," warns rival males away from its territory. The second, the "qui," attracts females. Unlike most frogs, the coqui skips the tadpole stage entirely. Eggs hatch directly into miniature froglets, each guarded by the father until they emerge. This unusual reproductive strategy eliminates the need for standing water, which is why the coqui thrives in the wet leaf litter of the forest floor rather than in ponds or streams. The species has become so central to Puerto Rican identity that the phrase "soy de aqui como el coqui" (I'm from here like the coqui) is a common expression of national pride.

The forest offers trails ranging from paved interpretive walks to muddy scrambles through dense cloud forest. The Pico El Yunque Trail climbs 1,748 feet over 5.4 miles to the summit of the mountain that gives the forest its name. La Coca Trail, at 1.8 miles, crosses so many streams and such thick foliage that more hikers get lost here than anywhere else in the park. La Mina Trail leads to the most photographed waterfall in the forest, though it remained closed years after Hurricane Maria shredded its canopy. At the El Portal Rainforest Center, a walkway 60 feet above the ground puts visitors at canopy level, face to face with the bromeliads, orchids, and ferns that cling to every available surface. Below, the rivers that Spanish miners once panned for gold run clear over boulders still bearing Taino petroglyphs.