Marine macroalgae are a polyphyletic group of photosynthetic eukaryotes and play critical roles in oxygen production, as primary producers, and in providing physical habitat structure. They harbor diverse microbial communities, including mutualistic, commensalistic, and parasitic fungi. These fungi may be obligately or facultatively marine and symbiotic. In this investigation, we isolated endophytic algicolous fungi from marine macroalgae collected from 5 intertidal sites in Nova Scotia. Fungi were cultured from surface-sterilized algal tissue and identified using ITS rDNA barcoding. From 21 marine macroalgal species collected, 11 algal species harbored endophytic fungi. We identified 23 endophytic algicolous fungi from the Bay of Fundy and Atlantic coasts of Nova Scotia. Marine endophytes are a promising new resource for bioactive compounds.