There is current taxonomic debate regarding its classification as an independent species or subspecies from that of the northern pygmy owl.

Similar plumage colour and different vocal patterns are the primary characteristics fuelling this confusion.

Although the International Union for Conservation of Nature (IUCN), has ranked this species as least concern, the increase in deforestation could impact the future population.

The taxonomy of the pygmy owl genus, (Glaucidium), remains disputed amongst taxonomic authorities.

[4] However, individuals inhabiting these regions demonstrate unique vocal patterns, indicating distinct species and population distribution.

[7] The head, neck, wings and tail have a pale rufous base colour, with a cream spotted pattern.

[8] The Guatemalan pygmy owl is distinguished by its vibrant red-brown plumage and white centre tail bars surrounded by a dark trim.

[8] There is limited information regarding specific seasonal calls or songs, pertaining to the mountain pygmy owl.

Territorial calls are considered primary and consist of an echoed single and or double "hooting/tooting", which can be heard close to sunrise and after sunset throughout the year.

[8] The diet of the mountain pygmy owl consists of the following: insects, orthopterans (crickets, grasshoppers), beetles, small mammals (rodents) and reptiles.

[5] Their diet consists of a large portion of songbirds including the American robins and larger species.

[9][7] Pygmy owls have a rather unique feeding habit, as they can consecutively consume prey head first.

[8] While perching on a high branch it will search for prey, and once found, the pygmy owl will dive to the ground to catch it.

It is significant to note that, if the attempt fails the owl will immediately search for new hunting grounds.

[10] The further northern pygmy owl species have a limited winter migration, descending from mountain regions to closer lowlands.

Once the eggs have hatched, the male mountain pygmy owl will provide more food to the female.

[8] It has been observed in several pygmy owl species that, within a month of hatching, 23–30 days, juveniles are able to fly and will leave their nests.

[8] The parental pair will remain in the vicinity of the nest, and provide protection for upwards of 20-30 additional days.

[8] According to the International Union for Conservation of Nature (IUCN) the mountain pygmy owl is categorized as a least-concern species.