The diversity of lignicolous freshwater fungi of China is currently being studied. In this paper, we report on nine collections of asexual morphs of Helminthosporium from submerged wood in rivers and streams in west to north-west Yunnan Province, China. The taxa are characterized based on morphology and phylogenetic analyses of ITS, LSU, SSU, RPB2 and TEF1α sequence data. A new species, Helminthosporium submersum, is described and illustrated with notes on taxonomy and phylogeny. Molecular data for Helminthosporium aquaticum and H. velutinum are provided.