Flagellar outer arm dynein from the ascidian, Ciona intestinalis, contains five intermediate chains (IC1-5). Molecular cloning of C. intestinalis IC3 shows significant sequence homology to the dynein intermediate chain (IC1) from sea urchin and human NM23-H8 protein. The N-terminal thioredoxin-related region is well conserved in the C. intestinalis IC3, sea urchin IC1, and human NM23-H8 protein. Three NDP kinase (NDPK)-related sequences are present in middle portions of both C. intestinalis IC3 and sea urchin IC1, but the human NM23-H8 protein had only two. A large part of the C-terminal glutamic acid-rich region present in sea urchin IC1 was greatly reduced in C. intestinalis IC3 and completely lost in human NM23-H8. Thus, thioredoxin/NDPK-related dynein intermediate chains (TNDK-DIC) would be a characteristic of metazoan flagella and they have become smaller in size and less acidic during evolution.