“The Encantadas, or Enchanted Isles” consists of ten “sketches,” or short accounts, about the Galápagos Islands. Each sketch describes either a particular island or a particular characteristic or inhabitant of an island. The sketches are based mostly on Melville's own experience as a sailor, having visited the Galápagos. Each sketch is preceded by several lines of verse, usually from Edmund Spenser's The Faerie Queene.

The first sketch describes the whole Galápagos region in general. The islands were formed by volcanoes, and are mostly dusty and barren, with a few lush spots here and there. They were once a popular resort for pirates raiding the South American coast. Because of their many peculiar features, some sailors believe the Galápagos to be "enchanted." The primary inhabitants of the islands are reptiles.

The second sketch describes three tortoises that were brought onto the ship. The narrator spent much time examining the tortoises, and was fascinated by them. The next day, the tortoises were killed and eaten, and their shells made into giant bowls.

The third sketch describes the “Rock Redondo,” a tall rock that stands on one of the islands. Over two hundred feet high, the rock provides an excellent view of the surrounding islands. The narrator lists the various sea birds that inhabit the Rock.

In the fourth sketch, the narrator climbs the Rock Redondo. As he invites the reader to gaze at the islands, he tells the story of how the Galápagos Islands were discovered, when mariners decided to sail farther out from the continent to avoid the dangerous currents from Peru to Chile.

The fifth sketch tells the story of the U.S.S. Essex and how, during the War of 1812, it spotted a ship near the Galápagos Islands. The captain believed it to be an enemy ship, although it unfurled an American flag; but as they approached, currents dragged the Essex away. When they returned, the ship had British flags flying. A sudden breeze allowed the ship to escape. It was never seen again, and so the sailors believed it was enchanted.

The sixth sketch describes Barrington Isle, a popular spot for pirates. It is small, but it has many plants, animals, and areas of fresh water, and it makes for good fishing.

The seventh sketch tells the story of Charles's Isle. It is almost as lush and productive as Barrington, and much larger. Charles's Isle was given to an adventurer who fought for Peru in its revolt against Spain. The adventurer called for pilgrims to populate the island, and he started a new colony. The adventurer took twenty attack-dogs with him. Soon the colony went sour, since criminals were amongst the colonists, he formed a bodyguard from some of the best men of the colony, but even they turned traitor, and finally a great battle was held between the colonists and the dogs. The adventurer lost and was exiled by the populace. As time wore on, the colony began to lure sailors away from unsuspecting ships that stopped at Charles's Isle for water or supplies, and soon any wise ship captain stayed away from the island.

The eighth sketch is another story, this one describing the “Chola widow,” Hunilla. The narrator's ship spots a lone woman on an island, and they pick her up. She had been marooned on the island months earlier when she and her husband, newly-wed, had been on a cruise. They had come near the Galápagos Islands, and the woman's husband and her brother had wanted to stay at one of the islands and collect valuable tortoise oil. The French captain agreed to drop them off with some supplies, and then to pick them up on his return trip four months later. The husband and brother had collected a lot of tortoise oil, so they decided to celebrate with a fishing trip in a makeshift boat. It sank, and both men drowned. The French ship never returned. The narrator's ship drops Hunilla off on the mainland, where they give her the money for the tortoise oil and a little of their own cash besides.

The ninth sketch tells the story of Hood's Isle and Oberlus, a hermit. Oberlus is a former sailor who deserted to Hood's Isle. He lived on the island growing small potatoes and other crops, which he sold to passing sailors. Eventually Oberlus fancied himself a king and wanted subjects, so he kidnaps four sailors and presses them into service, using his musket to frighten them into submission. He later arms them with cutlasses and leads them as pirates. One day, two large ships come in, sending four small boats to get supplies from Oberlus. Oberlus steals one of the boats. He escapes to the mainland of Peru, but his suspicious character gives him away, and he is thrown in jail.

In the tenth and final sketch, the narrator describes many of the runaways, castaways, and other human-related features of the islands, such as grave markers and messages-in-a-bottle.