Blake (1949) noted that specimens from both banks of the central Amazon (Óbidos and Santarém, both in Pará) differed from specimens from all other localities throughout the range of the species. Perhaps the most distinctive characteristic of these specimens is "gray vermiculation or freckling of the nuchal area, coverts, axillaries and middle rectrices"; almost all other specimens that he examined "can be distinguished by their somewhat more richly colored under parts, and by having the entire plumage, particularly that of the throat, more or less strongly diffused with rufescent buff that washes out much of the gray vermiculation found in Santarem and Obidos birds". The exception to this general pattern was a single specimen from "Pará" (= Belem) that was vermiculated with gray, similar to the birds from the central Amazon; other specimens from the same locality showed the expected rufescent tones to the plumage. Blake concluded that Spot-tailed Nightjar is monotypic but is "composed to two differentiated color 'phases' or plumage groups that attain varying degrees of dominance locally".
Described as Stenopsis maculicaudus by Lawrence (1862), with a type locality of Pará; the holotype is in the American Museum of Natural History (Greenway 1978).
This species later was transferred to Caprimulgus, a genus that eventually encompassed a large number of species of nightjars worldwide (Salvin and Hartert 1892, Peters 1940, Dickinson 2003). As field workers became more acquainted with maculicaudus in life, some questioned the allocation of maculicaudus to Caprimulgus (e.g. Davis 1962, Davis 1978, Howell and Webb 1995). Indeed, phylogenetic analysis of DNA sequence data, from both mitochondrial and nuclear genes, reveals that the broadly defined Caprimulgus of Peters (1940) and other authors is highly polyphyletic (Han et al. 2010). Caprimulgus proper is entirely confined to the Old World, and New World species of "Caprimulgus" are split into several clades.
"Caprimulgus" maculicaudus is revealed by Han et al. (2010) as basal to a clade that also includes "Caprimulgus" cayennensis (White-tailed Nightjar) and the genus Hydropalis. Hydropsalis is the oldest available generic name for this clade, so both maculicaudus and cayennensis are transferred from Caprimulgus to that genus.