Mussels in the subfamily Bathymodiolinae are common inhabitants of deep-sea chemosynthetic habitats, but in many places their diversity remains unknown. Here we describe Nypamodiolus samadiae n. gen. et n. sp. (Mytilidae: Bathymodiolinae) based on samples collected from the Haima cold seep in the South China Sea. Phylogenetic analyses based on fragments of three mitochondrial (cox1, 16S rRNA and nad4) and three nuclear (18S rRNA, 28S rRNA and histone H3) genes show that this new species belongs to a new genus, Nypamodiolus, which includes three named species (Myrina longissima Thiele and Jaeckel, 1931, Myrina simpsoni Marshall, 1900, Idasola japonica Habe, 1976) and a few undescribed species. Nypamodiolus n. gen. is characterized by small-sized, modioliform to fan-shaped shells with the umbones in a non-terminal position, and by robust anterior and posterior byssal retractor muscles arranged in roughly one plane. Most closely related to Nypamodiolus samadiae n. sp. is an undescribed species from the northern Papua New Guinea, to which it has a Kimura-2-parameter genetic distance of 11.8% for cox1. Sequencing the V3–V4 region of the microbial 16S rRNA gene reveals two dominant gill-associated bacteria in the new species, including one sulfur-oxidizing Gammaproteobacteria (relative abundance: 43.8–58.8%) and one unclassified Spirochaetes (relative abundance: 23.9–28.1%). Morphologically, N. samadiae n. sp. is similar to N. simpsoni, while can be distinguished by a larger maximum shell size (45.0 mm vs. 40.0 mm), larger length/height ratio (2.6–2.9 vs. 2.1–2.4), broader posterior end, slightly curved dorsal margin, and more anterior umbones.