Local architect-designer László Károlyi's beautifully restored mansion on the edge of the historic city center is certainly not the most hotel-y hotel in the capital (those would be the JW Marriott and the Swissôtel). For instance, there's no cable TV or AC in the 26 rooms (though there is a communal television in the lobby). It is, however, Quito's hippest lodging, a sanctuary of warm lighting, bemuraled walls (by the same artist who adorned Hacienda San Agustin), and theatrical Art Nouveau–ish detail, with a fantastic restaurant to boot. The rooms range from a tiny sunlit box with cavorting bulls painted on the walls to a generous corner honeymoon suite with a curtained king bed, fireplace, balcony, and claw-foot tub. (Go for the latter: It's a mere $20 or so more.) The hotel's rusty-ocher palette, candlelight, wood paneling, eccentric if well-intentioned service, and perfunctory attempt at soundproofing make the entire place feel like a fabulous stage set for some avant-garde production of A Midsummer Night's Dream.

Tucked into the Andean foothills amid a riot of bougainvillea and walnut trees, Hacienda Cusin is a rambling 16th-century estate that attracts Nobel Prize winners (scientist Murray Gell-Mann), actors (Meg Ryan), and pink tourists just back from the Galápagos. Owner Nick Millhouse, a chatty Brit, has worked since 1990 to convert the "fine ruin" into the current complex of stately dining halls, Spanish-style courtyards, and 42 guest rooms. Cozy taverns and creaky reading rooms are stuffed with objets d'art: Bolivian tapestries, afghan rugs, pre-Columbian pottery, and kooky murals. Guest rooms are simple, with folk art, writing desks, and handwoven blankets; instead of televisions, there are big windows that let in the light. Restless types can ride horses or mountain bike through fields cut by farmers whose descendants fought off the Incas. The Otavalo market, one of the best on the continent for indigenous wares, is just a 15-minute drive away.

Take a crash course in living Ecuadoran history at this most atmospheric of haciendas, site of the 1863 signing of the Treaty of Pinsaquí (the peace accord between Ecuador and Colombia) and still home to the same Freile-Larrea family who had the place built in the 1780s. The house is decked out with 18th-century French and Mexican antiques, crystal chandeliers, roaring fires, miles of marble and mirrors, and brocade chaise longues from which to contemplate the formal landscaped gardens. The showiest of the 29 rooms are in the main house; others, past the family chapel across the courtyard, are more rustic (though very comfortable and with their own fireplaces). Arriving groups get a welcome drink in the medieval cellar, where they'll likely be joined by the owner riding his favorite stallion down the stone steps. Photo ops ensue, with slightly drunk tourists sitting like toddlers on the long-suffering horse. The next day, they can ride for real; the property's stable has five horses. Non-equestrians can visit the nearby Otavalo market.

Occupying the site of a mid-15th-century Inca palace-fortress, parts of which are still being restored, San Agustin de Callo is today one of Ecuador's most luxurious haciendas. Owner Mignon Plaza (granddaughter of former president general Leonidas Plaza Gutierrez) lives on the property, and she's made the common areas richly comfortable. The living rooms are packed with rare manuscripts and monographs, antiques, plush couches, and photos of the hacienda's many renovations (in the 16th century, the property briefly housed an Augustine convent). The lodgings include 11 rooms spread through three buildings; the most atmospheric are those in the Inca House, which have cast-iron chandeliers, beamed ceilings, stone floors, claw-foot bathtubs, and views over the green Andean plains. Rooms in the newer Callo House and Cotopaxi House are also luxurious, with fireplaces and Jacuzzi tubs, but with a more modern aesthetic. At dusk, you can wander outside to watch the resident llamas grazing in the common courtyard, then repair to the volcanic-stone dining room for the nightly feast, presided over by a rotating cast of visiting chefs from around the world.

This beautiful late-17th-century hacienda is much more than a place to stay; it's a full cultural-immersion experience. If you score one of the nine rooms at the compound owned by the descendants of former president Galo Plaza Lasso, you become part of the family for the duration of your visit. This is one of only a handful of haciendas in Ecuador that are also working farms—dairy cows and sheep are tended here, and barley, quinoa, potatoes, wheat, and organic vegetables are grown on the property. This produce, plus fish from the on-site trout farm and cheeses, butter, and cream from the huge dairy, are incorporated into the food prepared by the family's genius chef, Jose Maria Pumsacho—making the dinner table here one of the best in the country. After the evening meal, you can ask whichever of the 21 Plaza Lasso cousins are available to take you round the estate to see the impressive gardens and cheese factory, or retire to your Architectural Digest–worthy room, decorated with framed, embroidered Zuleteño yokes and cuffs. Next day, arrange to take one of the hacienda's 90 horses (the Plaza Lassos have their own breed) out to the phenomenal mountainside Condor Rehabilitation Project, where the family is working to save the great Andean bird from extinction. You can also visit nearby pre-Inca archaeological sites like the Caranqui Pyramids.

An alternative to the forced march of the Galápagos cruise is the land-based stay, and this Isla Santa Cruz hotel sets you up nicely. On the ocean edge among wild mangroves near, but not in, downtown Puerto Ayora, it looks kookily Disney-esque, with its red adobe and kingfisher-blue curves, tree-cross-section tables, fanciful domed roofs, and sushi bar. The 12 rooms have built-in platform beds, terra-cotta tile or wooden floors, and bathrooms that seem hand-carved from rock (but are fully functional). The hotel organizes a menu of activities: exploring by 4x4, mountain biking, kayaking, horseback riding, surfing, and even scuba diving. There are also catered sleepover camps in tents, complete with cocktails and electricity. Remember to bring your $100 national park tax in cash, payable upon arrival.

Deep in the Amazon rain forest, on the banks of the Napo River between Puerto Misahuallí and Coca, is this unique micro-city. Built in 1995, the lodge is a branch of the Foundation for Education and Integral Development (FUNEDESIN), a nonprofit organization that works to educate and support the indigenous Montaña community. Yachana means "a place for learning" in the Quichua language, and indeed this environmentally friendly hotel plunges visitors into the indigenous lifestyle. Guests take river trips in dugout canoes, watch shamans perform healing ceremonies, learn about local flora and fauna, and eat local food, including Yachana Gourmet fair-trade chocolate (which, okay, you can also buy at Whole Foods Markets back home). This all takes place in relative luxury—relative being the operative word: Solar-powered lights and hot water, twin- or queen-size beds, closets, balconies, and hammocks are the extent of it. But this is the best place to be safely immersed in the fascinating and mysterious ways of El Oriente (not to mention the annual 12 feet of rain).