sec Y is a prokat~otic gone that encodes the SeeY protein, an integral membrane component of the prokaryotic protein translocation apparatus. A chloroplast-encoded see Y homologue has been identified in the unicellular, chromophytic alga, Pavlova lutherii. The gone predicts a protein composed of ten membrane-spanning regions, that is approximately 25% homologous and 50% similar to bacterial and plastid S¢¢Y proteins. The secl' gone from P. lutherli is independent of the ribosomal protein (rp) gone cluster to which it is closely linked in other organisms. In P. Iutherii see}" is located 5' to atpl and atpH. Since, in higher plants the atplHFA gone cluster and the rp gen0 cluster are s~paratcd by approximately 50 kb, we conclude, this indicates a novel chloroplast gone arrangement in P. lutherii.