An undertone is literally a muted tone of voice, but it can also refer to an unspoken, implied meaning or emotion: "I thought there were undertones of hostility in her supposed apology."
An undertone is a muted color or sound, like the blue undertones in your new gray wallpaper or the undertones of murmured conversations in a busy restaurant. When someone speaks in an undertone, it means that they whisper or talk very softly. You might tell you sister about your dad's surprise party in an undertone, so he doesn't overhear. These days, the word is most commonly used to refer to a subtle or implied meaning in an utterance.