Aquapteridospora lignicola gen. et sp. nov. was found on wood submerged in a freshwater stream in Chiang Rai Province, Thailand. Phylogenetic analysis of LSU sequence data placed the isolate in Diaporthomycetidae, genera incertae sedis. Aquapteridospora is a hyphomycete with polyblastic conidiogenous cells with several sympodial proliferations, bearing tiny, protuberant, circular scars and fusiform conidia, with pale to dark brown central cells and subhyaline end cells, sometimes with a conspicuous sheath. Aquapteridospora is compared to Pleurophragmium and Minimelanolocus which share some similar characters. A new genus and species is introduced to accommodate this new lineage with notes on its taxonomy and phylogeny.