During development of the embryonic zebrafish brain, the differential expression of axon guidance molecules directs the growth of axons along defined neuronal tracts. Neurons within the dorsorostral cluster of the presumptive telencephalon project axons ventrally along the supraoptic tract. Brother of Cdo (Boc) is a known axon guidance molecule that is expressed in a broad band lying ventral to the dorsorostral cluster of neurons. Loss of Boc function has previously been shown to perturb the development of the supraoptic tract. We have used live cell imaging of individual growth cones within the living zebrafish embryo to determine how Boc regulates the growth cone dynamics and axon guidance within the supraoptic tract. A plasmid construct encoding elavl3-eGFP was injected into early embryos to selectively label a small number of neurons while the expression of Boc was knocked down by injection of antisense morpholino oligonucleotides. Time-lapse imaging of growth cones within the living embryos revealed that loss of Boc significantly affected the morphology of growth cones in comparison to axons within control embryos. Growth cones navigating along the supraoptic tract in the absence of Boc extended significantly longer filopodia in the rostrocaudal direction. These results indicate that Boc acts to restrict axons and their filopodia within the narrow pathway of the supraoptic tract. The highly selective nature of these pathfinding defects reveal that Boc is likely to be one of many molecules that coordinate the trajectory of axons within the supraoptic tract.