In Ecuador's Amazon, your lodge's province decides the malaria advice.

Are there mosquitoes in Ecuador's Amazon? Yes, especially on forest trails, canoe trips and night walks, though screened cabins and bed nets keep the lodges themselves manageable. The province your lodge is in decides the CDC's malaria advice, and the yellow fever vaccine is recommended for all of them. Our Ecuador briefing covers the rest of the country.

Malaria: check your lodge's province

The CDC lists malaria prevention medicine for "Areas <1,500 m (<5,000 ft) elevation in the provinces of Cotopaxi, Esmeraldas, Morona-Santiago, Orellana, Pastaza, and Sucumbíos." Every other province has "Rare cases" below that height, and there the CDC recommends "insect bite precautions and mosquito avoidance only." The lodges all sit far below 5,000 feet, so the province decides it.

The name trips people up. "Napo" can mean Napo province, around Tena, or the Napo River, which flows on through Orellana past Coca to the lodges near Yasuní, so a "Napo lodge" can sit on either side of the line. Ask the lodge which province it is in, and take that answer to your clinic appointment.

Yellow fever: recommended in all three

The CDC's recommendation names every lodge province: "Vaccine is recommended for travelers ≥9 months old going to areas <2,300 m (7,550 ft) elevation, east of the Andes Mountains, in the provinces of Morona-Santiago, Napo, Orellana, Pastaza, Sucumbíos, Tungurahua, and Zamora-Chinchipe." PAHO counted 11 confirmed cases and 8 deaths in Ecuador in 2025, 3 of them in Sucumbíos, and the health ministry confirmed one in Orellana in 2026. Separately, Ecuador requires proof of vaccination from travelers aged 1 to 60 who have spent more than 10 days in Colombia, Peru, Brazil or Bolivia.

Dengue in the towns, mosquitoes on the trails

Dengue is mainly a town problem, carried by the day-biting Aedes mosquito in Coca, Lago Agrio and Tena. By late October 2026 the health ministry counted 994 cases in Napo province, the third-highest rate in Ecuador, with 69 in a single week and 2 deaths in Tena. Orellana had 626 and Sucumbíos 540. Wear repellent over sunscreen by day in the towns.

At the lodges, Cuyabeno's blackwater lagoons are often described as lighter on mosquitoes than visitors expect, while the trails around the lower Napo River lodges tend to be heavier. Night walks and canoe trips fall in the dusk-to-dawn hours of malaria mosquitoes and the sand flies behind leishmaniasis, which all three provinces reported in 2026. Wear permethrin-treated long sleeves, trousers and socks, tucked in, with repellent on exposed skin. Sleep under the net, and shake out boots and bedding in rustic lodges, where the bugs that spread Chagas disease can hide in palm thatch.

When to go

Rain falls in every month, and the CDC's advice applies all year. The drier stretch, roughly December to March, tends to be easier, and April to July tends to be the wettest. Dengue in the towns follows no fixed season.

Where you're going

Scores apply in any month.

Adding the islands? Our Galápagos briefing covers dengue in the island towns, where the CDC lists no malaria.

What travelers report

Paraphrased from TripAdvisor forum threads and a lodge review and linked so you can read them in full. One is from 2023 and the others are undated, and mosquito levels vary with the season, the lodge and the trail.

• Cuyabeno Reserve · August · 2023

  A trip report described a canoe ride down the Cuyabeno River to a lodge whose cabins were almost open-air, enclosed mostly by screens rather than walls, which kept mosquitoes out while allowing good ventilation. TripAdvisor ↗

• Cuyabeno lodge

  Asked about mosquitoes, one traveler said they saw none where they stayed in Cuyabeno, and another pointed out that the area is in Ecuador's malaria belt and suggested checking with a travel health provider. TripAdvisor ↗

• Napo Wildlife Center (Añangu, Orellana)

  A family reviewer said they had to use plenty of repellent and hiked through swarms of mosquitoes, called the night trip by canoe and on foot a great experience, and warned that the tower railing is not safe for children. TripAdvisor ↗

One rule outlasts the trip. Any fever during or after your trip means a doctor visit, and you tell the doctor you were in Ecuador's Amazon and in which province. Malaria can appear up to a year later, and a sore that won't heal needs a check too.

Traveler questions