It has been classified as critically endangered by BirdLife International, with an estimated population of 20–40 mature individuals in 2021, located in two large mangroves on Isabela.

The main predators of the mangrove finch are cats, fire ants, paper wasps, and especially destructive black rats and parasitic flies.

[4] By 2013, the avian vampire fly (introduced to the Galapagos Islands circa 1960s) had spread and killed about 55% of Darwin's finch nestlings within nests.

[1] In January 2014, project researchers reported successfully raising 15 mangrove finch chicks in captivity and releasing them back into the wild.

High rat abundance at breeding sites has led to substantial nesting failure due to predation and low fledgling success.

[1] The potential arrival of avian pox poses another significant threat to the species, as the mangrove finch lacks exposure and resilience to this disease.