The surface membranes of eukaryotic flagella and cilia are contiguous with the plasma membrane. Despite the absence of obvious physical structures that could form a barrier between the two membrane domains, the lipid and protein compositions of flagella and cilia are distinct from the rest of the cell surface membrane. We have exploited a flagellar glucose transporter from the parasitic protozoan Leishmania enriettii as a model system to characterize the first targeting motif for a flagellar membrane protein in any eukaryotic organism. In this study, we demonstrate that the flagellar membranetargeting motif is recognized by several species of Leishmania. Previously, we demonstrated that the 130 amino acid NH 2 -terminal cytoplasmic domain of isoform 1 glucose transporter was sufficient to target a nonflagellar integral membrane protein into the flagellar membrane. We have now determined that an essential flagellar targeting signal is located between amino acids 20 and 35 of the NH 2 -terminal domain. We have further analyzed the role of specific amino acids in this region by alanine replacement mutagenesis and determined that single amino acid substitutions did not abrogate targeting to the flagellar membrane. However, individual mutations located within a cluster of five contiguous amino acids, RTGTT, conferred differences in the degree of targeting to the flagellar membrane and the flagellar pocket, implying a role for these residues in the mechanism of flagellar trafficking.Eukaryotic flagella and cilia are present throughout the evolution of eukaryotic cells from early flagellated protozoa to mammalian cilia. These specialized organelles contain an internal microtubule-based axoneme that provides structure and generates movement (1, 2). Flagella and cilia play roles in cellular locomotion, trapping of food, and sensory functions (3). To carry out sensory functions, ciliary and flagellar membranes contain proteins unique to these organelles. For example, Caenorhabditis elegans expresses ODR-10 (a seven-transmembrane domain receptor), OSM-9 (a cation channel), and ODR-3 (a G␣ protein) that localize to the cilia of AWA olfactory neurons (4 -7). Mammalian ependymal cells, oviduct, and trachea contain a G protein subtype (G i2 ) that localizes predominantly in cilia (8). In addition to distinct protein compositions, considerable evidence has accumulated that flagella and cilia exhibit lipid compositions distinct from other domains of the plasma membrane (9). For example, Paramecium cilia contain 1.5 times more sterols and 5 times more sphingolipids relative to the lipid composition of the whole cell (9). Despite lipid and protein compositions distinct from the rest of the plasma membrane, the membranes of these organelles are contiguous with the plasma membrane. How these membrane subdomains are generated is a question of general importance in cell biology.Previously, several motile processes have been observed that could be responsible for movement of proteins into and within the flagellar membrane (3, 10, 11)....