Carcinin is a whey acidic protein (WAP) domain-containing antimicrobial protein produced by the circulating haemocytes of the shore crab, Carcinus maenas. Cloning of its full coding cDNA reveals that it shows some similarity to invertebrate defensins, has a valine-rich signal sequence followed by a defined cleavage site but no obvious acidic anionic ‘pro’ sequence. The C-terminus exhibits a unique cysteine array that is predicted to form six disulphide bonds in the tertiary structure. This 12 cysteine array arrangement is conserved in expressed sequence tags (ESTs) from related genera and seems to represent a novel tertiary structure amongst antimicrobial proteins (AMPs), unique to the Crustacea. There are at least five putative isoforms that arise through the transcription of a multi-exon gene. These isoforms do not arise as a result of alternate splicing of the exons, but by either the transcription of different alleles and/or single point mutation of the transcript at up to four loci in the gene. Several of the same transcripts have been found in different animals. The most commonly expressed transcript of the protein was recombinantly expressed in bacterial fusion system to a yield of ca. 2–3 μg ml−1 of culture. In vitro expression with or without the leader sequence confirms the bioinformatic prediction that the stability of the mature protein is reduced when the leader sequence is removed. Carcinin is one of very few invertebrate AMPs characterised at the gene, transcript and protein level and to be recombinantly expressed in vitro in a bacterial system.