Acetylcholinesterase exists predominantly as a secreted enzyme which remains cell-associated at specific extracellular locations. Its extensive structural diversity appears responsible for the unique cellular disposition of the enzyme. To examine the molecular basis of the structural divergence of acetylcholinesterase species, we hybridized total RNA from Torpedo californica electric organ with restriction fragments from a cDNA encoding the catalytic subunits of asymmetric species of acetylcholinesterase. Multiple RNA species up to 14 kilobases in length can be detected on Northern blots using a full-length cDNA for hybridization. Each of these RNA species also hybridizes with smaller restriction fragments within the open reading frame and 3'-untranslated region of the cDNA. This indicates that the entire open reading frame plus the 3'-untranslated region is contained in the large RNA species. RNase protection experiments revealed at least three points of divergence for the message species. One occurs within the COOH-terminal portion of the open reading frame at a position just 5' to the TGA stop codon. This divergence accounts for the two classes of acetylcholinesterase found in abundance in Torpedo. The site of splicing has been further defined by isolating a genomic clone containing the exon serving as the potential splice donor. We find a divergence between the cDNA and genomic DNA at the position estimated by the protection experiments. A less abundant divergence in mRNA can also be detected in the 3'-untranslated region. Another divergence occurs as a deleted sequence within the 5'-noncoding region and may be important for controlling translation efficiency. Since it is hypothesized that a single gene encodes acetylcholinesterase, the divergences in the very 3' region of the open reading frame and the 5'-noncoding region correspond to presumed splice junction boundaries where alternative RNA splicing occurs.