Analysis of sequence relationships in dynein heavy chains shows that dynein motor proteins comprise a single homologous family with three main branches, cytoplasmic dynein, axonemal dynein, and a third branch represented by DYH1B that lies between the other two. In all branches of the family the dynein heavy chain has four copies of the P-loop motif for a nucleotide-binding site spaced approximately 300 residues apart in its midregion, with the amino acid sequence GPAGTGKT in the P-loop of the hydrolytic ATP-binding site. Cytoplasmic dyneins appear more primitive in that the heavy chain usually occurs as a homodimer, with traces of the early evolution of its four P-loop motifs by gene duplication being recognizable. In the axonemal subfamily the heavy chain occurs as heterodimers or heterotrimers encoded by multiple genes, and their non-hydrolytic P-loop motifs are much more divergent with little trace of their origin by gene duplication. The DYH1B subfamily is more closely related to the cytoplasmic dyneins in sequence, but appears related to axonemal dyneins in function since it becomes upregulated during reciliation and has not been found in organisms, such as yeast and Dictyostelium, that are totally without cilia or flagella.