The internal transcribed spacer regions of the nuclear ribosomal DNA cistron of green algal endophytes, previously identified as Chlorochytrium inclusum Kjellman and Codiolum petrocelidis Kuckuck, were sequenced. Culture studies have implicated marine Chlorochytrium and Codiolum-like cells in the life histories of a number of macrophytic green algae. The identity of the endophytes was resolved by comparing DNA sequences from unicells endophytic in the foliose red alga Mazzaella splendens (Setchell et Gardner) Hommersand and in the crustose phase of Mastocarpus papillatus (J. Agardh) Kylin, with sequences from species of Acrosiphonia, Urospora, Ulothrix, and Monostroma. All endophyte isolates were more closely related to species of Acrosiphonia than to those of Urospora, Ulothrix, or Monostroma. The results support previous culture studies, and conclusively identify the endophytes obtained in the field as alternate life history phases of one or more Acrosiphonia species in southern British Columbia, Canada.