Acinetospora filamentosa and Microspongium stilophorae are reported as new records from South Korea based on morphological and molecular analyses. A. filamentosa is mainly characterized by having the sparsely branched erect filaments, the scattered meristematic zones, forming crampons, plurilocular sporangia on both prostrate filaments and lower part of erect filaments, and spherical to oval unilocular sporangia formed either sessile or with a pedicel. M. stilophorae is an epiphytic thalli mostly on Stilophora sp. It is characterized by prostrate filaments with irregular cells, short erect filaments with short ramuli, phaeophycean hairs, uniseriate plurilocular sporangia on the terminal part of erect filament. Our molecular analyses of rbcL and cox1 genes reveals that A. filamentosa and M. stilophorae are nested within the clades of Acinetospora and Microspongium, respectively.