The available genetic data, although limited, strongly suggests that the two subspecies of Lesser Wagtail-Tyrant are deeply divergent from one another, and that this species is paraphyletic with respect to Greater Wagtail-Tyrant Stigmatura budytoides (Harvey et al. 2020). Therefore we split this species: the Lesser Wagtail-Tyrant (Lesser) Stigmatura napensis napensis becomes Lesser Wagtail-Tyrant Stigmatura napensis; and the monotypic group Lesser Wagtail-Tyrant (Bahia) Stigmatura napensis bahiae becomes Bahia Wagtail-Tyrant Stigmatura bahiae. Revise the range of Lesser Wagtail-Tyrant from "Amazon system is. (se Colombia, e Ecuador, ne Peru and w Brazil)" to "along larger rivers of western and central Amazonia from eastern Ecuador (Napo River) and eastern Peru (Napo, Ucayali, and Amazon rivers) east to central Brazil (to the lower Tapajós River); also a population (possibly an undescribed taxon) in Orinoco drainages in extreme eastern Colombia (Vichada) and southwestern Venezuela (western Amazonas)".