The Cuban Macaw Ara tricolor was a species of macaw native to Cuba and Isla de la Juventud in the Caribbean that became extinct in the 1860s. Morphologically, it was similar to, but distinctively smaller than, the large red macaws – Scarlet Macaw Ara macao and Red‐and‐green Macaw Ara chloropterus. A close affinity with the Scarlet Macaw has been suggested based on plumage similarities. In this study we use complete mitochondrial genome sequences to examine the phylogenetic position of the Cuban Macaw. Our results do not indicate a sister‐species relationship with the Scarlet Macaw but place the Cuban Macaw as sister to the two red species and the two large green macaws, the Military Macaw Ara militaris and the Great Green Macaw Ara ambiguus. Divergence estimates suggests that the Cuban Macaw separated from this group approximately 4 million years ago.