Impacts on sea turtle populations from fisheries bycatch, climate change, habitat destruction and poaching have been widely discussed, but little is known about boat strikes as a potential threat to sea turtles. Here we present data on Pacific green turtles (Chelonia mydas) that suffered boat strikes in the Galapagos Marine Reserve at nesting beaches at Isabela Island and from foraging sites at San Cristobal Island from 2008 to 2011. Tourism in Galapagos has increased to more than 180,000 visitors a year and the boat traffic within the Marine Reserve poses a significant risk to sea turtles. Boat strikes were most frequent at foraging sites close to Puerto Baquerizo Moreno, a commercial and tourism port, where incidence varied between 16 and 20%. Incidence at nesting beaches was much lower with 3.7% of 4198 turtles showing injuries resulting from boat strikes. However, at the nesting beaches most of the impacts (59%) had occurred during the same nesting season while only 5% of the sea turtles observed at the foraging sites suffered their injuries during the study period. No data on survival rates from boat strike exist, however it is clear that many turtles die from the trauma caused by the impact. This report focuses on only the survivors; therefore the results represent a minimum estimate. Our study clearly shows that the overall threat from boat strikes has an important effect on the Galapagos green turtle population. Conservation management including speed limits in key turtle habitats are needed to improve their survival in the Galapagos Marine Reserve.