Here we describe an aetiocetid (toothed mysticete) from the Jinnobaru Formation (early Late Oligocene, about 28 million years ago) of Umashima, Kitakyushu, Japan. Oligocene mysticetes show an unparalleled diversity and morphological disparity in the evolutionary history of Mysticeti. However, the paleoecological aspects, such as the coexistence pattern, in the early mysticete evolution remain poorly explored. Our description of a toothed mysticete from the Oligocene of Umashima recognizes the first example of the coexistence of toothed and baleen-assisted mysticetes in the northwestern Pacific. Future finds of more Oligocene mysticetes should lead to a well-sampled dataset for analyzing the coexistence pattern or other related paleoecological traits to understand the demise of “archaic” Oligocene mysticetes and give rise to the modern-looking baleen whales.