Even when the Audiencia de Quito was created in 1563, there was a rumble of discontent from Lima over the position of the boundary - the first articulation of a tension that was to dog relations between the two countries for more than four centuries. As a part of the Viceroyalty of Nueva Granada in the early eighteenth century, the territory of the audiencia extended well into present-day Peru, far south of Tumbes and at least 200km east of Iquitos. After Independence, bitter fighting between the new states of Peru and Gran Colombia over their border resulted in the Mosquera-Pedemonte Treaty of 1830, which established a boundary along the ríos Huancabamba, Marañón and Amazonas all the way to Brazil. During the course of the nineteenth century, the vast eastern areas of rainforest were slowly populated by Peruvian settlers, who began to overwhelm what little Ecuadorian presence there was. The 1890 García-Herrera Treaty attempted to address this growing territorial problem, by splitting the region in half, but both Peru and Ecuador threw it out four years later. The King of Spain was called in to arbitrate, but he came up with a solution that left Ecuador even worse off, and the government rejected it outright, leaving the matter undecided. Shortly afterwards, Brazil annexed a chunk of Ecuador's remotest Amazonian lands, and a further slither was signed away to Colombia in 1916 through the Muñoz Vernaza-Suárez Treaty to resolve another border dispute. Six years later, the Colombians traded part of this territory to Peru - much to Ecuador's alarm - for navigation rights on the Amazon. Peru continued to expand into Ecuador's land during the early twentieth century and despite a series of talks and protocols in the 1920s and 1930s, the two countries failed to come to any agreement.

 

This set the stage for the Peruvian invasion in 1941, in which the ill-equipped Ecuadorian army was outnumbered five to one and unable to defend its huge Oriente territory as well as its southern provinces. Lima sent an ultimatum stating that it would only retreat from El Oro and Loja if Ecuador could come to a final agreement about the border. The result was the 1942 Protocol of Peace, Friendship and Boundaries between Ecuador and Peru, more commonly called the Rio Protocol , which gave almost half of Ecuador's territory to Peru.

The Ecuadorian government wasn't happy but had no choice other than to accept these terms, and so they did until 1947, when the US started taking aerial photos of the region and found a new river, the Cenepa , running between the ríos Santiago and Zamora. Ecuador soon seized on this discovery to bring the Rio Protocol into question. It stipulated that in the Cordillera del Cóndor the border be drawn at the watershed between the Santiago and Zamora rivers - but now the Cenepa made that division ambiguous. In 1951, President Galo Plaza said that the country did not recognize the border in this area, and in 1960, Velasco Ibarra nullified the entire protocol, severing all diplomatic links with Peru. From then on, Ecuadorian maps showed their territory as it stood before 1920.

During the 1970s, relations thawed somewhat after the foundation of the Andean Common Market (also known as the Andean Pact) in 1969, which joined together Ecuador, Peru, Colombia and Chile as trading partners. But by 1981, the old animosity had returned and fighting broke out along the 78km of disputed border in the Cordillera del Cóndor. Rodrigo Borja did much to heal the wounds when he invited the Peruvian president, Alberto Fujimori, to Quito in 1992, but just three years later an undeclared war erupted in the same region. The fighting was the worst seen since the 1941 attack, and for the first time in South American history, air-to-air combat was involved. At one stage, both countries claimed that they had control of a hill region in the midst of it called Tiwintza , but Ecuador pulled off a media victory by flying out international reporters to the area equipped with GPS devices to confirm their position and that Ecuador had control of it. After two months of fighting a ceasefire was agreed, and the Ecuadorian president, Durán Ballén, declared that the Rio Protocol was once again in operation, so laying the groundwork for a peace process.

On October 26, 1998, presidents Jamil Mahuad and Alberto Fujimori signed an historic peace treaty in Brasilia, setting the boundary over the contested 78km stretch, and bringing the long-standing dispute to an end. Although the border is little changed from that agreed in 1942, in a gesture of goodwill, Peru granted one square kilometre of its territory at Tiwintza to Ecuador as private property under Peruvian sovereignty, and will build a road linking it to the Ecuadorian border. The treaty also provides Ecuador with navigational rights on the Amazon and the establishment of two contiguous national parks on each side of the border. Furthermore, US$3 billion in international aid has been set aside to regenerate this region, so impoverished by years of dispute.