Trematosphaeria malaysiana sp. nov. is described based on light microscope and ultrastructural studies. It was found on driftwood, exposed test blocks of Avicennia marina and Rhizophora apiculata, and split twigs of R. apiculata exposed in Kuala Selangor and Morib mangroves, Malaysia. T. malaysiana is characterized by striate, pale brown ascospores and trabeculate pseudoparaphyses. Ascospore cell walls are two layered, an outer thick layer comprising fibrillar mucilaginous material, and an inner bilamellate layer (the inner layer electron-transparent; the outer electron-dense and containing melanin). Both T. malaysiana and Leptosphaeria pelagica were examined at the transmission electron microscope level and their structure compared with that of other bitunicate ascomycetes. T. malaysiana and L. pelagica were similar in that the mucilaginous sheath was the outer most layer, in the former the spore wall was two layered, while in L. pelagica it was three layered. In L. pelagica the spore wall was smooth, while in T. malaysiana it was longitudinally striate.