A phylogenetic analysis of morphological (osteological) characters of cormorants conducted by Siegel-Causey (1988) split Phalacrocoracidae into two clades: Phalacrocoracinae (cormorants) and Leucocarboninae (shags). The Guanay Cormorant was placed into the Leucocarboninae. Siegel-Causey placed Guanay in a clade (which he recognized as the genus Leucocarbo) with two AfricanSocotra Cormorant (nigrogularis) and Cape Cormorant (capensis); within this group, Siegel-Causey identified capensis as the sister species to bougainvillii.
Kennedy et al. (2000) conducted a phylogenetic analyis of DNA sequence data from the mitochondrial genes 12S, ATPase 6, and ATPase 12. With respect to bougainvillii, their phylogeny differed significantly from that of Siegel-Causey: they suggested instead that bougainvillii was a member of the clade of so-called blue-eyed shags, most of which occur in or near New Zealand - Campbell Island Shag (Phalacrocorax campbelli), Bronze Shag (Phalacrocorax chalconotus), Chatham Island Shag (Phalacrocorax onslowi), Stewart Island Shag (Phalacrocorax chalconotus), and Macquarie Island Shag (Phalacrocorax purpurascens) - but which also includes the Imperial Cormorant (Phalacrocorax atriceps albiventer) and Magellan Cormorant (Phalacrocorax magellanicus) of South America. Although Kennedy et al. (2000) found that bougainvillii always fit within the blue-eyed shag clade, its position within the clade was not stable.
Hybridizes locally with albiventer on the coast of Argentina (Devillers and Tershcuren 1978: 78, Bertellotti et al. 2003), where bougainvillii is rare.