Tourist-induced behavioural changes in large vertebrates are of concern for protected area management as they trigger a trade-off: large vertebrates attract visitors, but induced behavioral changes can reduce animal fitness and cause animals to avoid tourist-frequented zones. Behavioural response of animals to tourists is often studied to ensure informed management decision-making, a task frequently supported by flight distance analysis. In this context, guanaco (Lama guanicoe) response to tourists was studied in a protected area using two complementary methods: flight distance and sighting frequency analyses. Flight response analyses show that guanacos develop a considerable tolerance to vehicles and pedestrians in tourist areas, a reaction that extends approximately 500 m around visited areas. Such analyses thus point to (i) few areas being underused as a consequence of human presence and (ii) a low risk of tame animals being poached outside the park, all potentially leading to the conclusion that tourist visits are sustainable. However, guanaco sighting frequencies during 107 fieldwork days along 3 years show a significant reduction in sightings on days with higher Park visitor numbers. Moreover we present a formal procedure for the definition of a threshold for this to happen (247 visitors/day in our case). This suggests the potential risk of negative effects on guanaco population and a lower probability of guanaco sightings if Park visitor numbers rise beyond current figures. Results allow to conclude that assessment of human disturbance to flagship species in protected areas requires further methods in addition to flight distance.