It was previously classified in the Vochysiaceae family and elsewhere due to its unique floral features, but the APG III system of 2009 recognized Euphroniaceae as distinct and placed Euphronia in it.

[2] Based on molecular data from the rbcL gene, it is sister to the Chrysobalanaceae.

[3] The genus was originally described by Carl Friedrich Philipp von Martius and Joseph Gerhard Zuccarini in 1824 when they described Euphronia hirtelloides as a new species.

[6] And in 1987, the American botanist Julian Alfred Steyermark described the third species, Euphronia acuminatissima.

It was proposed in 1989 that the family Euphroniaceae be erected to contain the genus because it was sufficiently different from other related genera.