The main threat to the Mindo Harlequin Toad - rediscovered in 2019 after having last been seen in 1989 - is its extremely small and isolated population. The establishment and expansion of the Arlequín Reserve has already secured and restored the species' remaining known habitat, significantly reducing the immediate risk of habitat destruction. Due to a critically low population size, the species is now highly vulnerable to genetic bottlenecks, low reproductive success, environmental stochasticity, and disease outbreaks.
A key threat is Chytridomycosis, a deadly fungal infection of amphibians. First seen in Australia in 1993, it has affected about 30% of the amphibian species of the world, causing dramatic population declines and extinctions of amphibian species in North, Central and South America, eastern Australia, east Africa and the Caribbean. The fungus can cause 100% mortality in some populations. No effective measure is known for control of the disease in wild populations.