In this study, two endophytic fungal species were isolated from the marine green macroalga Codium fragile collected from the intertidal zones of Korea. The endophytic strains were isolated from asymptomatic, healthy algal tissues after surface sterilization. Based on morphological characteristics and multi-locus phylogenetic analyses using internal transcribed spacer regions, nuclear large subunit ribosomal DNA, nuclear small subunit ribosomal DNA, translation elongation factor 1-alpha, and RNA polymerase II second largest subunit genes, these isolates were identified as Paradendryphiella arenariae KNUE25A105 and Diaporthe novem KNUE25A206. This study provides the first detailed morphological and molecular phylogenetic descriptions of these two endophytic species from macroalgae in Korea, thereby expanding our understanding of the biodiversity of marine-derived endophytic fungi in temperate coastal environments.