Its natural habitats are subtropical or tropical moist lowland forest, subtropical or tropical moist montane forest, subtropical or tropical dry shrubland, and heavily degraded former forest.

The Cuban grassquit was formally described in 1789 by the German naturalist Johann Friedrich Gmelin under the binomial name Loxia canora.

[5] In the resulting reorganization, the Cuban grassquit was moved to the resurrected genus Phonipara that had been introduced in 1850 by the French naturalist Charles Lucien Bonaparte.

The specific epithet conora is from Latin canorus meaning "melodious".

[8] Although traditionally placed with the buntings and New World sparrows in the family Emberizidae,[4] molecular genetic studies have shown that the Cuban grassquit is a member of the subfamily Coerebinae within the tanager family Thraupidae.