Patterns of species abundance distribution (SAD) are driven by a given species’ physiology, life history attributes and environmental variables, and this is true of the Humboldt Penguin Spheniscus humboldti. Climate variability such as El Niño Southern Oscillation (ENSO) has impacted this species and other marine fauna in the eastern South Pacific Ocean. After reviewing manuscripts and reports, we identified 80 Humboldt Penguin breeding colonies, distributed from La Foca Island (05°12′S, 81°12′W) in Peru to Metalqui Island (42°12′S, 74°09′W) in Chile, but reduced the number to 73 after fieldwork surveys in northern Chile. At least three Humboldt Penguin colonies at the southern end of the Humboldt Penguin’s range also include Magellanic Penguins S. magellanicus. The Humboldt Penguin population of the main breeding colony in Peru, Punta San Juan, decreased 51% from 1980 to 2008, with notable decreases during El Niño. On the other hand, the population of Chañaral Island to the south increased 89% during the same period, which could be a result of irruption from more northern populations as well as past underestimation. The SAD does not follow the expected unimodal log-normal shaped model, and its shape has recently shifted significantly southward. This change is consistent with the species’ pattern of long distance movement during ENSO, reduced population genetic structure and long-distance gene flow between colonies, indicating the absence of philopatry, a decrease in population size in the main colonies in Peru and an increase in population size in colonies along northern Chile. The change in SAD might result from interactions between consecutive El Niño events, human activities and climate change. To better understand this pattern, further studies are required in population genetic structure, species physiology, and environmental variables in space and time.