A full-length chh cDNA was cloned from the eyestalk of Macrobrachium rosenbergii. The 991-bp cDNA contains an open reading frame of 408 bp that encodes the prepro-CHH. The tissue-specific expression pattern was examined by reverse transcriptase-polymerase chain reaction. Positive signals were detected in the eyestalk, heart, gills, antennal glands, and thoracic ganglion but not in muscle and hepatopancreas. However, two types of products were observed. The nucleotide sequences revealed the existence of 2 chh transcripts, named chh and chh- l, respectively. Direct sequence evidence suggests that these two isoforms come from a Chh gene transcribed in an alternative splicing manner. The Mar-Chh gene consists of 4 exons. The eyestalk transcript (chh) contains exons I, II, and IV, whereas the chh-l transcript in heart, gills, antennal glands, and thoracic ganglion contains all 4 exons. The appearance of exon III in chh-l cDNA changes the sequence content in the latter half of the mature peptide, starting within the codon of the 40th residue, arginine. The amino acid sequence deduced from exon III matched no homologue in public protein databases, while the 2 cysteine residues in this segment preserved the positional conservation characters of CHH neuropeptide family members. The common organization of Chh genes between palaemonid, brachyuran, and astacus crustaceans suggests that the Chh gene has a 4-exon structure in these species.