Nine subspecies generally are recognized (Dickinson 2003, König and Weick 2008). The following synopsis is based on König and Weick (2008):
M. c. choliba (Vieillot 1817): Occurs in southern Mato Grosso and São Paulo, Brazil, south to eastern Paraguay.
M. c. luctisomus (Bangs and Pernard 1921): Occurs from the Pacific slope in Costa Rica south to the Canal Zone in Panama, and on the Pearl Islands.
M. c. margaritae (Cory 1915): Restricted to Margarita Island off of northern Venezuela. Paler than nominate choliba.
M. c. crucigerus (Spix 1824): Occurs from eastern Colombia, Venezuela, and Trinidad east to the Guianas and south to eastern Peru. Body feathers have fluffy yellowish spots.
M. c. duidae (Chapman 1929): Confined to upper forested slopes of Mount Duida and Mount Neblina in southern Venezuela. This is a very dark subspecies with a rather uniform crown and a broken, whitish, collar on hindneck; this is the only subspecies of Tropical Screech-Owl with a white band across that back of the neck. Perhaps represents a separate species.
M. c. decussatus (Lichtenstein 1823): Occurs in central and southern Brazil. Smaller and paler than crucigerus, with whitish spots on the mantle.
M. c. uruguaiensis (Hekstra 1982): Occurs in southeastern Brazil (Santa Catarina, Rio Grande do Sul), northeastern Argentina and in Uruguay. Shaft streaks on underparts are rather prominent; body feathers with buffy-rufous downs.
M. c. surutus (L. Kelso 1941): Found in Bolivia. Brighter rufous than crucigerus, and the streaks and bars are more reduced.
M. c. wetmorei (Brodkorb 1937): Occurs in the chaco of Paraguay and Argentina, south to Mendoza and northernf Buenos Aires. Darker than decussatus and underparts more dirty-buff.