We describe M. fujianensis n. sp. (Annelida: Hesionidae), collected from the coast of Fujian Province, China, based on morphological and molecular analyses. Micropodarke fujianensis n. sp. is characterized by having two pairs of minute eyes, and neurochaetae of middle segments without basal long teeth. The K2P distances of COI, 16S rRNA, 18S rRNA, 28S rRNA, and histone H3 fragments diverged from the corresponding sequences of the closest related species of Micropodarke in GenBank and BOLD Systems by 22.3%, 10.7%, 0, 1.15%, and 1.1%, respectively. Among the Micropodarke species with such DNA sequences for comparison, M. fujianensis n. sp. is most closely related to M. cf. dubia-a species collected from Daya Bay, China. An updated key to Micropodarke species is provided.