Composed of two subspecies: A. x. xanthomus breeds on Puerto Rico; A. x. monensis, described by Barnés (1945), breeds on Mona Island. Plumage of A. x. monensis is similar to that of nominate xanthomus, except lesser wing coverts paler yellow, and middle wing coverts extensively or entirely white, or "very pale yellowish white." Juveniles are "almost fully alike" adult individuals of A. x. xanthomus.
The species was described by Sclater, who named it Icterus xanthomus (1862, Collection of American Birds, page 131), based on specimens collected on Puerto Rico.
The Yellow-shouldered Blackbird and Tawny-shouldered Blackbird (A. humeralis) of Cuba and northwestern Haiti constitute a superspecies (Sibley and Monroe 1990). Lanyon (1994), Lanyon and Omland (1999), and Barker et al. (2008) used phylogenetic analysis of mitochondrial DNA (cytochrome b) to investigate the relationships within Agelaius blackbirds. They all identified two clades in Agelaius, a North American group (phoeniceus, tricolor, and assimilis) and a Caribbean group (xanthomus, humeralis).