Calmodulin is encoded in Chlamydomonas reinhardtii by a single gene that 1) has multiple intervening sequences, 2) has 5' structural motifs that are phylogenetically conserved, 3) contains 5' sequences that are similar to those found in genes of some transforming, cytoskeletal, and stress-response proteins, and 4) produces at both life cycle stages, a single size class of mRNA and proteins that are identical in amino acid sequence. Based on the amino acid sequence of calmodulin from the vegetative phase of the life cycle, synthetic oligonucleotide probes, containing inosine in order to reduce codon redundancy, were used to detect and isolate cloned cDNAs coding for the gametic phase calmodulin. The complete DNA sequence was elucidated and shown to code for a protein identical to the vegetative phase protein. Analysis of the production of calmodulin mRNA indicates that protein production is under quantitative regulation and possibly coupled with the synthesis of other proteins in the flagellar apparatus. The full length cDNA was used to isolate overlapping genomic clones that include the entire calmodulin transcriptional unit and 5' regulatory sequences. The complete DNA sequence of the gene, including all intron sequences, was elucidated. The DNA sequence of the coding regions shows some phylogenetic conservation. Finally, there are regions of 5' sequence reminiscent of sequence motifs recently identified as binding sites of transcriptional regulatory proteins. Overall, these studies suggest possible molecular genetic relationships between calmodulin, a transducer of intracellular calcium signals, and other proteins involved in eukaryotic cell structure, motility, and homeostasis.