Application of a fluorescent dye to a target area of axons or dendrites allows the identification of individual neurons projecting to the area and reconstruction of the tract of the neurite by retrograde labeling. For the red fluorescent dye tetramethylrhodamine dextran, the labeling occurs by active retrograde transport inside the cell. This protocol describes a method for applying tetramethylrhodamine dextran to living zebrafish embryos and larvae (2-7 dpf [days post-fertilization]) via microinjection. It may be adapted for use with green or yellow fluorescent dextran conjugates.