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Noteworthy species endemic to the Galapagos Islands off Ecuador are two flightless birds, the Galapagos Penguin (Spheniscus mendiculus) and Flightless Cormorant (Phalacrocrax harrisi). Both adapted increased swimming ability at the cost of flight. This however has limited their ability to find richer feeding grounds in times of low resource availability, or to escape potential predators. Their population numbers, though small, were stable. Stress on this stability has increased since human arrival. Various invasive species from pets, farm animals and rats to even mosquito vectors of avian disease accompanied humans. . El Nino Southern Oscillation or ENSO cycles of warm waters in the Pacific Ocean south of the Equator cause drastic drops in food sources for all Galapagos seabirds. Serious ENSO events in 1983 and 1998 caused some species’ populations to drop by as much as 77%. Periodic less severe cycles may help explain how population recovery has not rebounded to earlier numbers. Reduced chick survival and adult fecundity seem to occur in concert with mild events. With available data and use of a modeling approach, this study focuses and explores their situations. Restoring population stability may include use of models, species monitoring, conservation and limiting invasive species. Usher matrices based on different climate conditions were produced using data combined from current and past census counts and weather. Models are used to compare available census data and test reliable predictors. Climate data from National Oceanic and Atmospheric Administration and the University of Florida provides for testing predictions of current and probable future climate change. Life histories of both species are regarded. Results suggest the current Cormorant population is still stable. The Penguin, however, faces a 20% probability of extinction in 100 years if current conditions remain. Extinction probability rises to 60% if climate change continues to worsen. Interventions such as captive breeding could be suitable for population recovery.