Selaginella submonospora is described as a new species from western Yunnan (China) based on morphological and molecular evidence. It is morphologically similar to S. subdiaphana (Wall. ex Hook. et Grev.) Spring, S. monosporaSpring, and S. hezhangensis P. S. Wang et X. Y. Wang. Selaginella submonospora can be distinguished by its leaves with short denticulate-ciliolate margins, dorsal leaves obliquely subcordate at base, short acuminate at apices, and ventral leaf oblique at base. Furthermore, the phylogenetic analysis based on the concatenated chloroplast genes rbcL, atpI, and psbA supported that S. submonospora is a distinct species and closely related to S. monospora.