Does anybody know if there is a flight from Iquitos to Guayaquil in Ecuador? I would like to do the Amazon from Iquitos and then galapagos rather than the Amazon in Ecuador (no idea why though)
No, in fact I believe that the only flights from Peru to Guayaquil are from Lima (not even from Trujillo).
Since Iquitos is still claimed from Peru by Ecuador after losing it in a series of wars and other disputes stretching from independence to a serious war in 1941 (and still not resolved), it would be political suicide for the Ecuadorian government to permit such a connection.
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