A parasite species of the genus Plasmodium has recently been documented in the endangered Galapagos penguin (Spheniscus mendiculus). Avian malaria causes high mortality in several species after initial exposure and there is great concern for the conservation of the endemic Galapagos penguin. Using a Plasmodium spp. circumsporozoite protein antigen, we standardized an enzyme-linked immunosorbent assay to test the level of exposure in this small population, as indicated by seroprevalence. Sera from adult and juvenile Galapagos penguins collected between 2004 and 2009 on the Galapagos archipelago were tested for the presence of anti-Plasmodium spp. antibodies. Penguins were also tested for the prevalence of avian malaria parasite DNA using a polymerase chain reaction (PCR) screening. Total seroprevalence of malarial antibodies in this sample group was 97.2%, which suggests high exposure to the parasite and low Plasmodium-induced mortality. However, total prevalence of Plasmodium parasite DNA by PCR screening was 9.2%, and this suggests that parasite prevalence may be under-detected through PCR screening. Multiple detection methods may be necessary to measure the real extent of Plasmodium exposure on the archipelago.