The nouns overtone and undertone—usually pluralized, overtones and undertones—should logically be opposites, but they are effectively synonyms when used to mean an underlying or implied quality or meaning. The words are often used interchangeably.
Overtone has a music-related definition—a musical tone that is higher than the fundamental tone—that it does not share with undertone. And undertone has a definition—a hushed tone or sound—that it does not share with overtone. But when it comes to the sense synonymous with hints, suggestions, or intimations, overtones and undertones have little difference.
Examples
In contrast to the debate in the U.S., net neutrality has not taken on ideological or political overtones in Europe. [Wall Street Journal]
Like in Tropico 3, the sinister undertones of totalitarian oppression and corruption inTropico 4 are largely offset by the tongue-in-cheek tone. [Paste Magazine]
Many, however, fear that the electoral battle could assume divisive religious and sectarian overtones. [Financial Times]
The movie has met with mixed reviews and some critics have taken aim at the film’s erotic undertones. [Sydney Morning Herald]