Craspedodidymum nigroseptatum sp. nov. is described and illustrated based on specimens collected on decaying rachides of Oncosperma horridum in Brunei Darussalam. It differs from other species of Craspedodidymum in producing dark brown conidia with three to four thick, darkly-pigmented septa, and a paler basal cell. Conidia are broadly ellipsoidal to obovoid and truncate at the base. Craspedodidymum nigroseptatum is compared with other species in the genus and a key to the genus is provided.