A new species of lizardfish, Synodus nigrotaeniatus, n sp., is described from Lembeh Strait, North Sulawesi Province, Indonesia on the basis of six specimens, 129.7–233.5 mm SL. Diagnostic features include 11–12 (usually 12) dorsal-fin rays, 12–14 anal-fin rays, 13 pectoral-fin rays, 47–49 lateral-line scales, 48–49 total vertebrae, a deep suborbital pore with prominent surrounding fimbriae, and a rudimentary adipose fin that is scarcely visible without magnification. The new species is an apparent close relative of S. sageneus (mainly Australian distribution, but records from Sri Lanka, Bali, and West Papua), sharing most morphological and meristic features. Nevertheless, the two species differ in markings, with S. sageneus lacking the black midlateral stripe that is a key feature of S. nigrotaeniatus. The new species has a slightly wider interobital space than S. sageneus (mean 4.4% vs. 3.5% SL) and slightly lower vertebral and lateral-line scale counts (48–49 and 47–49 respectively, vs. usually 51–54 and 51–55). Both species possess a well-developed suborbital pore, but the surrounding fimbriae of S. nigrotaeniatus are more numerous, sometimes branched, and extend upwards along the rear margin of the eye, compared to those of S. sageneus, which are generally fewer, thicker, and shorter, and do not extend along the posterior edge of the eye.