In vertebrate many vertebrate species, the development of early axonal tracts in the forebrain is well conserved and stereotyped: two ventral longitudinal tracts, the tract of the postoptic commissure (TPOC) and the medial longitudinal fasciculus (MLF) are first laid down during the initial stages of anterior brain development. We report that a putative transmembrane protein, ISLR2 (immunoglobulin superfamily containing leucine-rich repeat 2) is uniquely expressed in ventral longitudinal tracts in the forebrain of chick embryos. During early developmental stages, ISLR2 protein was expressed in the longitudinal tracts, including the TPOC, the mamillo-tegmentum tract (MTT), and the MLF. Using ISLR2 mRNA in situ hybridization, we located the origins of these longitudinal tracts and found that each source of the tracts was represented as a unique neuronal population in previously described compartments in the forebrain region. Interestingly, ISLR2 protein has a consensus sorting signal to endosomes. Consistent with this, ISLR2 protein was localized in endosome-like intracellular organelles, but not in the cell surface membrane, when ISLR2 protein was expressed in vitro. In cultured dorsal root ganglion cells, ISLR2 protein was also observed in vesicle-looking intracellular organelles. These data suggest that ISLR2 may contribute to understanding for studying molecular mechanisms of longitudinal axonal tract formation as well to phylogenetic studies of neuromeric organization in the forebrain.