The plastid of Euglena gracilis was acquired secondarily through an endosymbiotic event with a eukaryotic green alga, and as a result, it is surrounded by a third membrane. This membrane complexity raises the question of how the plastid proteins are targeted to and imported into the organelle. To further explore plastid protein targeting in Euglena, we screened a total of 9,461 expressed sequence tag (EST) clusters (derived from 19,013 individual ESTs) for full-length proteins that are plastid localized to characterize their targeting sequences and to infer potential modes of translocation. Of the 117 proteins identified as being potentially plastid localized whose N-terminal targeting sequences could be inferred, 83 were unique and could be classified into two major groups. Class I proteins have tripartite targeting sequences, comprising (in order) an N-terminal signal sequence, a plastid transit peptide domain, and a predicted stop-transfer sequence. Within this class of proteins are the lumen-targeted proteins (class IB), which have an additional hydrophobic domain similar to a signal sequence and required for further targeting across the thylakoid membrane. Class II proteins lack the putative stop-transfer sequence and possess only a signal sequence at the N terminus, followed by what, in amino acid composition, resembles a plastid transit peptide. Unexpectedly, a few unrelated plastid-targeted proteins exhibit highly similar transit sequences, implying either a recent swapping of these domains or a conserved function. This work represents the most comprehensive description to date of transit peptides in Euglena and hints at the complex routes of plastid targeting that must exist in this organism.A fundamental problem in cell biology is the precise and efficient targeting of proteins synthesized by cytoplasmic ribosomes to their appropriate intracellular locations. Proteins destined for the endomembrane system, mitochondria, or the chloroplast usually have specific N-terminal targeting domains that are required for proper subcellular localization. These leader sequences are often removed by specific proteases at the protein's destination prior to it assuming its active conformation. For chloroplast-targeted proteins in plants and algae, an N-terminal transit peptide (TP) is both necessary and sufficient for correct plastid targeting (11). Transit peptides are not conserved in sequence but exhibit characteristic biochemical properties, such as an elevated content of the hydroxylated amino acids serine and threonine as well as a deficiency of acidic (aspartate and glutamate) amino acids (76). Within a typical chloroplast, there are six distinct locations to which the constituent proteins must be sorted, and some proteins have to cross up to three membranes (33). This complexity requires additional targeting information within the transit peptide, such as the signal sequence-like domain found in proteins targeted to the thylakoid membrane, or information contained within the mature portion of the protein itself...