A new crop of affordable boutique hotels is coming to some of Southeast Asia’s less traveled shores. Just 50 miles east of Singapore is Nikoi Island (beach houses from $190), a 37-acre private isle off the coast of Bintan fringed by powdery white-sand beaches. Its 10 Indonesian-inspired bungalows are constructed from driftwood and outfitted with built-in daybeds, stone-floored bathrooms, and thatch roofs. On Siargao Island, in the southeast corner of the Philippines, two Paris transplants recently opened Kalinaw Resort (villas from $130), a haven for surfers and Manila urbanites. The property’s five airy beachfront cottages have dark doyok-doyok–wood floors and small balconies with rattan hammocks. Not far from the coast of Malaysian Borneo you’ll find Bunga Raya Island Resort (doubles from $600, including meals and speedboat transfers), a secluded jungle hideaway that includes 56 timbered villas—some with private plunge pools—set in a lush rain forest. The 32 villas at Thailand’s Seven Seas Resort (villas from $188), a two-hour drive from Krabi, have open-air rain showers and terraces, many of which look out over the Andaman Sea.