The Southeastern Pacific Humpback whale Megaptera novaeangliae reproduces from June to September off the coast of Ecuador where a large artisanal fisheries fleet consisting of more than 15,000 vessels operates year round. The bycatch impact on this humpback population has been overlooked. Based on the annual bycatch mortality documented in this study, about 0.53% (95% CI 0.2-1.5%) of the population might be potentially bycaught in gillnets annually. Depending on the total population numbers estimated and reported elsewhere for this stock (2917 or 6277 whales), the bycatch mortality is equivalent to 15 or 33 whales per year. A significant correlation was found between the annual bycatch rate and fishing effort for the period 2000-2009 (r=0.68, p<0.05). An increase in artisanal fisheries may cause drastic consequences since humpback whales as K-strategists have low birth and survival rates. Calves are probably the most threatened age class due to gillnet entanglements in proximity to coastal waters where artisanal vessels operate. The Ecuadorian breeding grounds for humpback whales migrating from Antarctica might become a hot spot for bycatch in the Southeastern Tropical Pacific, if the bycatch rate continues to increase. Urgent mitigation strategies coupled with precautionary management and conservation measures are required to protect this vulnerable stock of whales in the long term. The consequences of humpback whale bycatch off coastal Ecuador and possible solutions to mitigate the bycatch are analyzed.