The Hispaniolan euphonia was formally described in 1789 by the German naturalist Johann Friedrich Gmelin in his revised and expanded edition of Carl Linnaeus's Systema Naturae.

[2] The specific epithet is from Latin musicus meaning "musical" or "musician".

[3] Gmelin based his account on "L'organiste", a bird from Saint-Domingue, a French colony on the island of Hispaniola, that had been described in 1778 by the French polymath the Comte de Buffon in his multi-volume work, Histoire Naturelle des Oiseaux.

[4] A hand-coloured engraving by François-Nicolas Martinet was published separately to accompany Buffon's text.

[6] A molecular phylogenetic study published in 2020 found that the "blue-hooded" euphonias, the Hispaniolan, elegant and golden-rumped euphonias, formed a distinct clade that was sister to the genus Chlorophonia.