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Taxonomic frameworks for medically important species such as cobras (genus <i>Naja</i> Laurenti, 1768; Squamata, Elapidae) are essential for the medical treatment of snake bites and accurate antivenin development. In this paper, we described the former <i>N. kaouthia</i> populations recorded from China as a new species and designated a neotype for <i>N. atra</i>-based morphological and mitochondrial phylogenetic analysis. The new species <i>N</i>. <i>fuxi</i><b>sp. nov.</b> was morphologically diagnosed from <i>N. kaouthia</i> by (1) regular single narrow crossband present on the middle and posterior parts of the dorsum (3–15, 7.9 ± 2.7, <i>n</i> = 32) and the dorsal surface of the tail (1–6, 4.2 ± 1.1, <i>n</i> = 32) of both adults and juveniles, buff-colored with dark fringes on both edges, vs. South Asian populations (<i>n</i> = 39) and Southeast Asian populations (<i>n</i> = 35) without cross bands, with irregular cross bands or multiple light-colored crossbands pairs, or densely woven lines; (2) small scales between the posterior chin shields, usually three (40%) or two (37%), rarely four (13%), or one (10%) (<i>n</i> = 30) vs. mostly one (81%) and rarely two (19%) (<i>n</i> = 28); (3) ventrals 179–205 (195.4 ± 6.7, <i>n</i> = 33) vs. South Asian populations 179–199 (188.7 ± 5.9, <i>n</i> = 12); Southeast Asian populations 168–186 (177.8 ± 4.9, <i>n</i> = 18). Phylogenetically, the new species forms an independent sister clade to the clade including <i>N. atra</i>, <i>N. kaouthia</i>, <i>N. oxiana</i> and <i>N. sagittifera</i>. Furthermore, the subspecies <i>N. naja polyocellata</i> should be resurrected and recognized as a full species, <i>N. polyocellata</i><b>comb. nov.</b>, and the subspecies <i>N. sumatrana miolepis</i> should be resurrected.