Scolecobasidium is cosmopolitan and includes species that inhabit a wide range of ecosystems including soil, water, air, plant and cold-blooded vertebrates. During a fungal survey from mangrove, strains of Scolecobasidium occurring on leaf spots of true mangrove plants, Aegiceras corniculatum and Acanthus ebracteatus, were isolated from Futian Mangrove in Shenzhen and the Qi’ao-Dangan Island Mangrove in Zhuhai, China. Unlike most species in Scolecobasidium that produce dark conidia, our strains are characterized by hyaline to pale brown conidia and inconspicuous thread-like sterigmata. Further detailed morphological comparison and multi-locus (LSU, ITS, tub2, tef1-α) phylogenetic analyses revealed these collections as two new taxa, namely S. acanthisp. nov. and S. aegiceratissp. nov. We further emend the generic description of Scolecobasidium, propose one new combination, S. terrestre comb. nov., and clarify the taxonomic status of S. constrictum.