Archipel I: Route AB

San Cristobal's airport sits at the edge of Puerto Baquerizo Moreno, a five-minute drive from the town center, so this is usually your first taste of the islands rather than a standalone excursion. Sea lions and marine iguanas are known to rest right next to the runway here, an unscripted welcome few airports can match. From the terminal, a short transfer takes you down to the pier for a panga ride out to your ship.

Formed by geological uplift rather than volcanic activity, Santa Fe is unusually flat for a Galapagos island, and it's the only place on Earth with its own endemic subspecies of land iguana. After landing in clear, turquoise water, a walk through a forest of giant, tree-sized Opuntia cactus leads to iguanas basking beneath them. The Galapagos dove is a reliable sight along the trail, and with some luck you may also spot the Galapagos snake or the Galapagos hawk.

A dry landing sets you down on North Seymour's flat, sun-baked terrain, and the trail wastes no time getting to the action: magnificent frigatebirds display from low shrubs right along the path, males inflating their scarlet throat pouches into balloons to catch a female's eye. Blue-footed boobies are a near-constant presence along the same stretch, and during the breeding season you may catch their high-stepping courtship dance just a few feet from the trail, showing off the bright blue feet that give the species its name. Land and marine iguanas share the coastline as the trail loops back toward the water, and sea lions haul out along the shore. Keep an eye on the cliffs above the surf too, where swallow-tailed gulls sometimes perch between flights out to sea.

Despite the name, Los Gemelos aren't volcanic craters. They're twin sinkholes, formed when empty underground magma chambers collapsed, set in the misty highlands of Santa Cruz and ringed by dense, endemic Scalesia forest. A trail loops around both rims through some of the lushest vegetation in the islands, one of the better places in the archipelago to spot a short-eared owl hunting in daylight, and, with patience, the increasingly rare vermilion flycatcher.

At first glance Punta Moreno looks like little more than a lava flow at the base of Cerro Azul, but its black surface holds a series of lagoons with a surprising amount of life. Flamingos are a fairly good bet in the pools, and paint-billed crakes, white-cheeked pintails, and common gallinules turn up for those willing to watch the water closely.

Fernandina is the only major island in the archipelago with no introduced species, which makes Punta Espinosa one of the most pristine wildlife encounters anywhere in the Galapagos. A wet landing brings you onto black lava draped with the largest gathering of marine iguanas in the islands, alongside Galapagos penguins and flightless cormorants, both drawn here by the cold, nutrient-rich current. Around June, when marine iguana hatchlings emerge, keep an eye out for the Galapagos racer snake hunting along the nesting zone. Snorkeling here is a rare chance to watch marine iguanas feeding underwater, a behavior found almost nowhere else.

Puerto Egas stands out for its black volcanic sand and a shoreline where land and sea meet in close quarters. Galapagos hawks are often seen along the walk, and at the far end waits a colony of Galapagos fur seals tucked into shaded rock grottoes, one of the more reliable places in the islands to see this endangered species.

Reachable only by sea, Black Turtle Cove is a mangrove-lined lagoon on Santa Cruz's north shore, protected as a turtle sanctuary. A slow, quiet dinghy ride carries you between four species of mangrove while sea turtles surface for air around the boat, one of the most reliable sightings in the islands. Look down and you'll often see golden and eagle rays moving beneath the hull, and white-tipped reef sharks resting in the shallows.

A stone stairway carved into the cliff climbs to a wide plateau holding one of Genovesa's largest seabird colonies. The trail passes through a small Scalesia forest, home to the short-eared owl, one of the few predators on the island, before reaching cliffside colonies where Nazca and red-footed boobies nest side by side, frigatebirds wheel overhead, and thousands of storm petrels dart in and out of cracks in the lava. A small colony of fur seals sometimes gathers near the landing. Red-footed boobies nest in only a handful of places across the archipelago, and this is one of them.

A wooden staircase of 372 steps climbs Bartolome's extinct volcano from a lava-and-concrete dock or sandy beach, depending on conditions. Along the way, red, orange, black, and even green volcanic layers mark the slopes, home to pioneer plants like the island-endemic Tiquilia nesiotica, lava cactus, and scattered Scalesia. With some luck, a lava lizard crosses the trail. At the top, the view over the twin bays and the iconic Pinnacle Rock is the reward for the climb. Back at sea level, a snorkel around the coral reef and submerged lava rocks is a good bet for Galapagos penguins and white-tipped reef sharks, with sea turtles and manta rays turning up now and then too.

Despite the name, Los Gemelos aren't volcanic craters. They're twin sinkholes, formed when empty underground magma chambers collapsed, set in the misty highlands of Santa Cruz and ringed by dense, endemic Scalesia forest. A trail loops around both rims through some of the lushest vegetation in the islands, one of the better places in the archipelago to spot a short-eared owl hunting in daylight, and, with patience, the increasingly rare vermilion flycatcher.

From the landing, a trail leads to a wide, shallow lagoon where Galapagos flamingos wade through the shallows, filtering shrimp from the mud that gives them their color. Continuing over a low rise brings you to Flour Beach, a nesting ground for green sea turtles between December and June. Just offshore, the eroded remains of an old volcanic cone form Devil's Crown, one of the best snorkeling spots in the islands. White-tipped reef sharks and spotted eagle rays are a near-certain sight inside the ring, and on a good day you might also spot hammerhead sharks, sea lions, or a colorful mix of reef fish weaving through the rocks.

A short landing on one of the most beautiful beaches in the islands brings you into a resident colony of Galapagos sea lions, sprawled across the white sand. Between August and November you may also spot pups nursing nearby. This is one of the only places to see the Espanola mockingbird, found nowhere else on Earth and famously unbothered by visitors. After time on the beach, a relaxed snorkel just offshore is a good way to close out the visit, with spotted eagle rays often gliding beneath the surface.

Punta Pitt is the only site in the islands where all three Galapagos booby species nest within view of one another: red-foots in the low trees, Nazca boobies on the open cliff-edge ground, and blue-foots further inland. A steep gully climbs to the breeding grounds, where frigatebirds often circle overhead and swallow-tailed gulls round out the colony.

A short crossing from Puerto Baquerizo Moreno on San Cristobal, Isla Lobos takes its name from the sea lion colony that calls it home, and doubles as a seasonal nesting ground for blue-footed boobies. Frigatebirds have begun nesting here in recent years too, and fur seals turn up now and then. The walk covers roughly 850 meters of mixed rocky and sandy trail.