SecY is a component of the protein-conducting channel for protein transport across the cytoplasmic membrane of prokaryotes. It is intimately associated with a second integral membrane protein, SecE, and together with SecA forms the minimal core of the preprotein translocase. A chloroplast homologue of SecY (cpSecY) has previously been identified and determined to be localized to the thylakoid membrane. In the present work, we demonstrate that a SecE homologue is localized to the thylakoid membrane, where it forms a complex with cpSecY. Digitonin solubilization of thylakoid membranes releases the SecY/E complex in a 180-kDa form, indicating that other components are present and/or the complex is a higher order oligomer of the cpSecY/E dimer. To test whether cpSecY forms the protein-conducting channel of the thylakoid membrane, translocation assays were conducted with the SecA-dependent substrate OE33 and the SecA-independent substrate OE23, in the presence and absence of antibodies raised against cpSecY. The antibodies inhibited translocation of OE33 but not OE23, indicating that cpSecY comprises the protein-conducting channel used in the SecA-dependent pathway, whereas a distinct protein conducting channel is used to translocate OE23.Thylakoid membranes consist of proteins synthesized by both nuclear and chloroplast genomes. Nuclear encoded thylakoid proteins are first targeted to the chloroplast by means of the transit peptide, which initiates the translocation of the protein across the envelope membranes into the stroma (1). Translation initiation of chloroplast encoded thylakoid proteins appears to occur in the stroma (2, 3), and then synthesis appears to continue on thylakoid bound ribosomes through a co-translational targeting mechanism (4). Considerable progress has been made in defining mechanisms by which nuclear encoded thylakoid proteins insert or translocate posttranslationally across the membrane. One class of proteins insert into the membrane in the absence of an energy supply, soluble factors, or membrane components (5-8). A second class of proteins does not require any soluble factors but requires a transthylakoid pH gradient and the membrane protein encoded by