The Galapagos Flycatcher is presently listed by IUCN as an LC (“Least Concern”) species. The bird seems to be reasonably abundant on most islands and anywhere that its habitat occurs.
Almost all of the flycatcher's habitat is protected lands incorporated into Galapagos National Park, with only highland areas where the species appears to be naturally less common not included in the park. Therefore, it seems that habitat loss is unlikely to be a significant threat to the species. The species's propensity for nesting in cavities, and especially in cavities in cacti or in power-line poles probably protect its nests somewhat from predation by the introduced rats and cats. The most serious threat to the flycatcher may be from introduced parasites or diseases. Currently, the most likely threat is from the introduced botfly Philornis downsi, which causes significant mortality, morbidity, and malformation in nestlings of other species, such as the Darwin's finches (Dudaniec et al. 2006).