The little pied cormorant was originally described by French naturalist Louis Jean Pierre Vieillot in 1817. In 1931, American ornithologist James Lee Peters was the first to consider this in a separate genus along with the pygmy cormorant ("M. pygmaeus"), little cormorant ("M. niger"), and the long-tailed cormorant ("M. africanus"). Since then, molecular work by Sibley and Ahlquist showed the little pied and long-tailed cormorants formed a group which had diverged early on from other cormorants. This group of "micro-cormorants" assumed the genus name "Microcarbo", initially described by French naturalist Charles Lucien Bonaparte in 1855. The generic name is derived from the Ancient Greek "mikros" "small", and Latin "carbo" "black". However, most older authorities refer to this species as "Phalacrocorax melanoleucus".