Allen (1889) described Conopophaga rusbyi from a single specimen in female plumage from Reyes, El Beni Department (not La Paz Department; Peters 1951), Bolivia which, if valid, would presumably be a subspecies of Black-bellied Gnateater, but rusbyi has not been considered a valid taxon by most subsequent authors (Hellmayr 1907, 1910, Brabourne and Chubb 1912, Cory and Hellmayr 1924, Whitney 2003).
Described as Conopophaga melanogaster Ménétries 1835; type locality "Cuyaba" = Cuiabá, Mato Grosso, Brazil. This locality designation for the type (male) is considered an error and has been emended to Rio Madeira, Brazil (Hellmayr 1910, Cory and Hellmayr 1924).
The species is named for the distinctive all-black underparts of the males.
Due mostly to its larger size, Chubb (1918, 1921) separated Black-bellied Gnateater into its own genus, Pseudoconopophaga. This separation was not followed by subsequent authors, however, as there are no other clear differences.
Whitney (2003) suggested, primarily based on vocal similarities, that Black-bellied Gnateater is most closely related to the lineata group, comprised of Conopophaga lineata (Rufous Gnateater), Conopophaga roberti (Hooded Gnateater), Conopophaga peruviana (Ash-throated Gnateater), Conopophaga ardesiaca (Slaty Gnateater), and Conopophaga castaneiceps (Chestnut-crowned Gnateater).
Some authors have misspelled the specific epithet as "melanogastra" (e.g., Sclater 1858, 1890).