Galápagos penguins (Spheniscus mendiculus) and flightless cormorants (Phalacrocorax harrisi) live in small, isolated populations on the westernmost islands of Isabela and Fernandina in the Galápagos Islands, Ecuador. Between August 2003 and February 2005, 4 field trips, 2 in the cool, dry season (August 2003 and August 2004) and 2 in the hot, rainy season (March 2004 and February 2005), were undertaken; 298 Galápagos penguins and 380 cormorants were sampled for prevalence and intensity of hemoparasites. Microfilariae were found in both the penguins and the cormorants. Blood smears were negative for the presence of other species of hemoparasites. Overall prevalence of microfilariae across seasons was 42.0% in cormorants and 13.8% in the penguins. Intensity of infection was generally low (mean = 3.2–31.7 in 25 fields across seasons and species) with the exception of a few individuals with markedly high intensities of parasites (>300 in 25 fields in 1 cormorant). Prevalence of microfilariae increased significantly over the 4 sampling periods for cormorants, but not for penguins. Prevalences were significantly higher in cormorants than in penguins for 3 of the 4 collecting trips. Male penguins had higher prevalences than females; however, there were no gender differences in cormorants. No relation was detected between body mass and either presence or intensity of parasitism. Morphological characteristics of the microfilariae are also described and specimens from each host species were similar in all characters measured. DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene were consistent with the morphological evidence and together demonstrate that the penguins and cormorants are likely to be infected with the same species of microfilariae.