The poorly known marine ascomycete Manglicola guatemalensis from Trang and Trat provinces, Thailand, were collected in 2005 and 2006 on the brackish water palm Nypa fruticans. This fungus is known only from two previous collections. This paper reports on the morphological characteristics and molecular phylogeny of this unique marine bitunicate ascomycete. Manglicola guatemalensis has large clavate to obtusely fusiform ascomata, wide ostioles, bitunicate asci, cylindrical, thick-walled, unequally one-septate ascospores, constricted at the septum, apical cell larger, chestnut-brown and a smaller light brown basal cell. Ascospores germinate readily, always from the basal cell. Four isolates from different locations were selected for the phylogenetic study. Regions of the rDNA gene, including SSU and LSU, were sequenced and combined. Molecular data places M. guatemalensis in the Jahnulales with high bootstrap support; all strains are monophyletic. In the combined SSU and LSU analyses the Jahnulales comprises four subclades, A, B, C and D. Subclade A comprises Jahnula species and two anamorphic fungi, Brachiosphaera tropicalis and Xylomyces chlamydosporus. In subclade B Manglicola strains form a sister group of the Aliquandostipite species Aliquandostipite crystallinus, A. khaoyaiensis, Jahnula siamensiae and Patescospora separans. Subclade C comprises Jahnula species, Jahnula aquatica, J. granulosa and J. rostrata, while Megalohypha aqua-dulces constitutes subclade D. Therefore Manglicola forms another lineage of marine fungi.