A new species of splitfin fish, Synagrops atrumoris sp. nov., from Dongsha Island, Taiwan, South China Sea, is described based on its morphological characteristics, including osteology and otolith morphology, and DNA sequence. Synagrops atrumoris sp. nov. is closely similar to Synagrops japonicus and can be distinguished by its black mouth cavity covering the lower portion of the tongue, posteriorly enlarged and complex basioccipital fossae, and a triangular otolith with a strong postero-dorsal angle, as well as a strong genetic difference. In addition, the taxonomy of the genus Synagrops was revised. Available published data, together with our results, suggest that S. bellus is a synonym of S. japonicus.