In modern Japanese, ateji (当て字, 宛字 or あてじ, literally "assigned characters") primarily refers to kanji used phonetically to represent native or borrowed words, without regard to the meaning of the underlying characters.
The term ateji is also used for the opposite process, writing words using kanji for meaning only, without regard to the reading.
For example, sushi is often written with the ateji 寿司. Though the two characters are respectively read as su and shi, the character 寿 means "one's natural life span" and 司 means "to administer", neither of which has anything to do with the food.
An example of the opposite process (meaning only) is 煙草 (tabako) for "tobacco", where the individual kanji respectively mean "smoke" and "herb" but have no phonetic relationship to the word tabako. This is also considered a kind of ateji.
Jukujikun can be considered a form of ateji.