In the last two decades, more than 35% of coastal wetlands in the tropics and subtropics have been destroyed, mangrove forest being the most affected habitat. However, mangroves have been poorly studied around the world, particularly in the Neotropics. The spatio-temporal diversity of the mangrove bird community in the Jambelí archipelago, in southwestern Ecuador, was studied. Between 2 August 2015 and 25 July 2016, a total of 118 species (35 migratory and 83 resident species) belonging to 44 families were documented. Nine of the 83 resident species are endemic to the coasts of Ecuador and northwestern Peru; six are threatened species. The most abundant species in the archipelago were Magnificent Frigatebird (Fregata magnificens) and Neotropic Cormorant (Phalacrocorax brasilianus), while the best represented family was Laridae (n = 12 species). No spatial or temporal differences in bird diversity were detected (P > 0.35). The Jambelí archipelago has a high diversity of bird species, particularly as a wintering and stopover site for boreal migratory species. A long-term monitoring program for bird populations in the area has been proposed as an effective tool to assess the conservation status of this important and threatened ecosystem.