The fuel surcharge for a Galapagos cruise is a rather complicated affair, as it has nothing to do with the retail price of gasoline or diesel in Ecuador. Fuel prices in Ecuador have been subsidized by the Ecuadorian government for quite some time. In 2008, for the first time, the government decided to adjust their fuel subsidization policy by issuing decree #921, taxing (or lifting the subsidy on) all Galapagos yachts that use more than 4000 gallons of fuel per month.
This decree was handed down in Spring, 2008, with virtually no warning, effective June 1, 2008. The tax applies to all yachts that use more than 4000 gallons/month, and all of these yachts have been forced to add a fuel subsidy to their prices for 2008-9 to compensate for this last-minute government tax. Some yachts avoided this tax because they use less than 4000 gallons/month due to a central island (not visiting Isabela, Fernandina, Genovesa, etc) itinerary and/or small boat size, while the rest had to pass it on to their passengers.
So, the smaller yachts with central islands itineraries aren’t affected by the fuel surcharge. The boats with the more comprehensive itineraries (including Genovesa and/or Isabela), and the larger, more comfortable boats, are all affected by the government’s fuel policies.
The fuel surcharge won’t go away until the government changes its policy regarding subsidies, and it doesn’t appear this is going to happen in te forseeable future. Until then, fuel surcharges will be common on the larger, more comfortable boats with the best itineraries.