The genus Haligena (Halosphaeriales, Ascomycota), with two accepted species, is encountered frequently in marine habitats, especially on wood in temperate regions. Phylogenetic analyses of Haligena elaterophora (type species) and H. salina were undertaken, with partial large subunit ribosomal DNA sequences, to determine their relationships with other closely related genera in the order. The genus was shown to be polyphyletic within the Halosphaeriales with the type species forming a basal clade to the order. Haligena salina constituted a sister clade with weak support of Neptunella longirostris in all analyses. Haligena elaterophora and H. salina differ significantly in the nature of their ascospore appendages: wider, more sticky and strap-like in H. elaterophora and spoon-shaped at the point of attachment; in H. salina they are longer and narrower, finely drawn out filaments. A new genus, Morakotiella, is introduced to accommodate H. salina.