We applied a capture–mark–resight (CMR) method to estimate the population size of the Galápagos Penguin Spheniscus mendiculus. In 1999, we estimated 1198 individuals, with lower and upper 95% confidence limits of 1054 and 1403 individuals, respectively, and estimated that approximately 57% of the total population was counted in an annual census. Applying this estimate to the 2003 census, we estimated that the population size for the whole archipelago was 1351 individuals. We also applied the correction factor derived from the 1999 CMR data to other censuses carried out between 1970 and 2003 and estimated a maximum population of about 4000 individuals in 1971 when the highest numbers of Penguins were counted. Although the Penguin population size has fluctuated in the last 33 years, the overall trend shows larger populations in 1970–80 followed by relatively smaller populations and a slow recovery rate in 1983–2003. The data set also shows two major population declines (in 1983 and 1998), which are coincident with El Niño episodes.

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