On a smaller budget, you could stay at Francisco Inn, where prices are about 30C$ per night on average. A cheaper option would be Spin Designer Hostel, close to Freediving Dimension, and with a sundeck and a sunbathing terrace.
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Catian Beach Resort is a 3-star property that will put you a few steps from Big Lagoon El Nido and Nacpan Beach in Nacpan Beach district.
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El Gordo'S Adventures And Guesthouse is a modest apartment, located a 10-minute walk from Artcafe. La Salangane Caalan Beach Villa is a great B&B with views of the garden, located within a short walk of El Nido Party Boat. If you're traveling on business, a convenient option is Devia Lodge Elnido, which welcomes to book a room at 41C$ per night. If you are specifically interested in snorkeling and diving, book a resort such as Plankton Divers - Zions Welcome Inn near Palawan Freedivers, which is only a 30-minute walk away.