Long-finned pilot whales in the Strait of Gibraltar are distributed over the main shipping routes. This exposes them to risks of collisions and probable acoustic and physical disturbance. This species is also the target of whale-watching operations. The aim of this study was to estimate the annual population size, survival rate, and population growth rate of pilot whales occurring in the Strait and their inter-annual variation using photo-identification. A robust design was used to estimate all three parameters. A total of 10,784 individual pilot whale fins were photographed and analyzed. The population size estimation in summer ranged from a low of 147 individuals in 1999 to a high of 265 individuals in 2003. The annual population growth rate was estimated from mark recapture models to be 5.5%. The survival rate of adults was estimated at 0.982 (95% CI: 0.955–0.993). The same individuals have been observed between years. This suggests that this population is resident in the Strait, at least during summer. This study provides baseline knowledge prior to a predicted increase in shipping traffic throughout the main foraging area due to the opening in 2007 of a major shipping harbor along the Moroccan coast of the Strait.