The IUCN Red List status of the Altamira Yellowthroat is Vulnerable due to its small population and distribution and its dependence on patchy wetland habitats (a distribution of 51,900 km²; BirdLife International 2014). It is considered Endangered under Mexican law (NOM-059 SEMARNAT 2010). Altamira Yellowthroat also is considered a species at greatest risk of extinction by Partners in Flight (Berlanga et al. 2010). Based on determinations of habitat loss, Berlanga et al. (2010) estimated that 50% or more of its population has been lost in Mexico during the last century.

Altamira Yellowthroat is dependent on specialized conditions in freshwater marsh habitats. The primary threat to this species is draining of wetlands and other ecosystem modifications.