Amphibian populations around the world have been declining at an alarming rate due to factors such as habitat destruction, pollution, and infectious diseases. Between May and July 2008, we investigated a fungal pathogen in the critically endangered Morelet's treefrog (Agalychnis moreletii) at sites in El Salvador. Larvae were screened with a hand lens for indications of infection with Batrachochytrium dendrobatidis (Bd), a fungus that can cause lethal chytridiomycosis in amphibians. Subsets of inspected tadpoles were preserved for analysis by polymerase chain reaction to determine the effectiveness of hand lens screening for presence of Bd and to estimate infection prevalence at various sites. Because individuals with signs of infection were preferentially included, we used a novel method to generate unbiased estimates of infection prevalence from these biased samples. External mouthpart deformities, identified with a hand lens, successfully predicted Bd infection across a large spatial scale. Two of 13 sites sampled had high (≥ 89%) estimated prevalence, whereas little or no Bd was detected at the remaining sites. Although it appears that A. moreletii populations in this region are not suffering rapid declines due to Bd, further monitoring is required to determine the extent to which these populations are stably coexisting with the pathogen.