Genes expressed specifically in a tissue are often involved in the defining functions of that tissue. We used representational difference analysis of cDNA to amplify 20 cDNA fragments representing transcripts that were more abundant in the lobster olfactory organ than in brain, eye/eyestalk, dactyl, pereiopod, or second antenna. We then independently confirmed that the transcripts represented by these clones were enriched in the olfactory organ. The 20 cDNA fragments represent between 6 and 15 different genes. Six of the cDNAs contained sequences highly similar to known gene families. We performed in situ hybridization with these six and found that all were expressed in subsets of cells associated with the aesthetasc sensilla in the olfactory organ. Clones OET-07, an ionotropic receptor, and OET-10, an alpha tubulin, were specific to the olfactory receptor neurons. OET-02, a monooxygenase, was expressed only in the outer auxiliary cells. OET-03, a serine protease, was specific to the collar cells. OET-11, an alpha(2) macroglobulin, was expressed by the receptor neurons and the collar cells. OET-17, a calcyphosine, was expressed in the receptor neurons, inner auxiliary cells, and collar cells. The identities and expression patterns of these six transcripts predict involvement in both known and novel properties of the lobster olfactory organ.