Endophytic fungi (EF) are endophytes that have symbiotic interactions with their host plants without bringing any pathogenic effects. They can improve the pathogenic resistance of host plants by supplying bioactive metabolites. Mangroves live and adapt according to zonation due to their resistance ability towards the harsh intertidal environments. This is thought to result in EF that are able to produce different secondary metabolites depending on the habitat of the host plants. In the present study, we aim to profile and compare the secondary metabolites of the endophytic fungus Pyrrhoderma noxium isolated from three different mangrove species, namely, Avicennia alba, Bruguiera gymnorrhiza, and Sonneratia alba, and identify their potential bioactivities. Methanol extracts of P. noxium cultured on potato dextrose agar were analyzed via liquid chromatography-mass spectrometry (LC-MS) system. Our results indicated the presence of various metabolites with reported bioactivities, including phenols, alkaloids, terpenoids, etc. Interestingly, differences in the composition of secondary metabolites were found between the three different mangrove host plants. Based on published literature, the bioactivities of the secondary metabolites identified include antibacterial, antiprotozoan, antiviral, anti-inflammation, and cancer-inhibiting properties. This study has not only shed light on the potential bioactivities of secondary metabolites extracted from mangrove EF, but also the potential of the same species of EF isolated from different host plants to produce varying secondary metabolites.