Mangroves are relatively unexplored habitats and have been shown to harbour a number of novel species of fungi. In this study, samples of microfungi were collected from symptomatic branches, stem and leaves of the mangrove species Xylocarpus granatum, X. moluccensis and Lumnitzera racemosa and examined morphologically. The phylogeny recovered supports our morphological data to introduce three new species, Cytospora lumnitzericola, C. thailandica and C. xylocarpi. In addition, a combined multi-gene DNA sequence dataset (ITS, LSU, ACT and RPB2) was analysed to investigate phylogenetic relationships of isolates and help in a more reliable species identification.