Worldwide, 32 species have been recognized in the genus Neosiphonia. We describe two new species of the genus from Bali, Indonesia, based on morphological and molecular data. Neosiphonia baliana sp. nov. is recognized by having rhizoids cut off from the proximal end of pericentral cells, axes with five pericentral cells, axes ecorticate throughout, the absence of trichoblasts and scar cells, the straight arrangement of tetrasporangia, and spermatangia arising from a basal cell without the production of trichoblasts. Neosiphonia silvae sp. nov. is characterized by having rhizoids cut off from the proximal end of pericentral cells, axes with four pericentral cells, axes ecorticate throughout, production of abundant trichoblasts near the apices, prominent scar cells, an exceedingly prominent apical cell at axis tips, and one or two tetrasporangia per branch. Phylogenetic analyses of rbcL indicated that our N. baliana sp. nov. and N. silvae sp. nov. fall in the genus Neosiphonia, and we distinguish them on the basis of morphological features from other congeneric species.