Island species typically exist in pathogen and predator sparse environments before human settlement, and are particularly vulnerable to the impacts of invasive species. In this study, we used the variable circular-plot method to estimate the density of birds in the highlands of Floreana Island, Galápagos Archipelago, where introduced parasites, predators, and habitat degradation are a known threat to endemic species. We recorded the number of birds seen and heard at 15 locations near Cerro Pajas Volcano in 2004 and 2008, an area that harbours the largest expanse of highland Scalesia forest on Floreana Island. We estimated the change in population density for nine bird species, including five species of Darwin’s finches. We specifically address changes in population density for the locally endemic Medium Tree Finch Camarhynchus pauper, which only occurs on Floreana Island and has a small population size. Comparing 2004 and 2008, our study found lower population density in the Medium Tree Finch, but stable population density in Small Tree Finch C. parvulus and Large Tree Finch C. psittacula. Based on data from three additional highland sites surveyed in 2008, we estimate that the maximum size of the Medium Tree Finch population is 1,620 individuals. In addition to the survey data, we observed breeding males in 2006 and 2008. We found: (1) low nesting success (six out of 63 nests produced fledglings) and high Philornis downsi parasite intensity, and (2) a biased age structure of the breeding population. No breeding males were one year old in 2006, and no males were five years old in either study year, indicating low reproductive success as well as limited lifespan. This research has contributed to the recent re-evaluation by IUCN, which has changed the Red List status of the Medium Tree Finch from ‘Vulnerable’ to ‘Critically Endangered’.