Black Skimmer taxonomy has been subject to confusion and debate. Griscom's (1935) study of museum specimens aimed "to solve the geographic anomalies and taxonomic difficulties which various writers have emphasized for many years". Although five subspecies of Black Skimmer have been described (Griscom 1935, Murphy 1936), only three currently are recognized (Wetmore 1944, Blake 1977).
The three subspecies are:
niger, described as Rynchops nigra Linneaus 1758; type locality "America", restricted to coast of South Carolina. Includes intermedia Rendahl 1919 and oblita Griscom 1935.
Breeds in North America (United States and Mexico), wintering from the southern United States to Panama and Guadeloupe.
Characterized by smaller size, white wing lining, and a white tail with dark central feathers (Gochfeld and Burger 1994). Has broad white edgings on the secondaries (Wetmore 1944).
cinerascens, described as Rhynchops cinerascens Spix 1825; type locality Amazon River, Brazil.
Generally the subspecies of northern South America east of the Andes, breeding from Colombia east to the Guianas, and south to Bolivia and Amazonian Brazil. ,
Larger than the other two subspecies. Underwing is “light sooty gray, secondaries much less conspicuously tipped with white” (Murphy 1936). Referred to as the “brown or sooty-tailed race” with its dark brown, white-edged tail (Gochfeld and Burger 1994).
intercedens, described as Rhynchops intercedens Saunders 1895; type locality Säo Paulo, Brazil.
Breeds from south central and northeastern Brazil south to central Argentina and the La Plata estuary.
Sometimes referred to as the southern Black Skimmer (e.g., Coelho Naves and Vooren 2006), or the "white-tailed race" (Gochfeld and Burger 1994). Larger than niger, and inner webs of lateral rectrices are tinged brownish gray, except for adults in breeding plumage (Griscom 1935). Like niger, has white underwing coverts and secondaries broadly tipped with white (Gochfeld and Burger 1994), and with the lighter, medium-brown of the central tail compared to the other races.
A study of the genetic structure of Black Skimmers in southern South America (subspecies interdecens) used six microsatellite loci to compare breeding populations in Brazil and Argentina, along with individuals from the main nonbreeding site in Argentina. Only weak genetic differentiation was found among colonies, even though there are two distinct breeding phenologies (see Breeding), which might be due to the effect of a very important nonbreeding site in southern South America that is shared by these populations (Mariano-Jelicich and Madrid 2014). In other words, intermingling at that site might results in gene flow among populations. However, their data also suggest that populations in the south are not entirely panmictic.