Nipponitrigonia yebisu sp. nov. is a newly described species from the mid-Cretaceous Goshoura Group on Shishi-jima and Goshoura-jima islands, Kyushu, Japan. This species is characterized by its smooth shell surface ornamentation, lacking concentric costae near the umbo and anterior part of the shell surface, in contrast to other known species. The shell inflation shows considerable intraspecific variation. The species occurs from the Mortoniceras sp. Zone of the upper Albian to the Graysonites adkinsi–Desmoceras kossmati Zone of the lowermost Cenomanian and would have survived to the Turonian. Nipponitrigonia yebisu sp. nov. occur from gravelly sandstone and conglomerate in upper shoreface environment, in which the valves are usually disarticulated. We discovered five still-articulated individuals. Among them, three individuals were interpreted in situ, recording the burial orientations (direction and plunge angles of the commissure planes and marginal carina). According to the burial position, their posterior edge area was oriented upward, and the plunge angles after tilt correction were approximately 10–20 degrees to the bedding. This burial position closely resembles that of extant Neotrigonia species, and it is suggested that these individuals were buried in situ in a high-energy depositional environment. Nipponitrigonia tends to lose shell ornamentation stratigraphically, and Nipponitrigonia yebisu sp. nov. is the last representative of the genus as far as known.