The cardinal feature of neuronal polarization is the establishment and maintenance of axons and dendrites. How axonal and dendritic proteins are sorted and targeted to different compartments is poorly understood. Here, we identified distinct dileucine motifs that are necessary and sufficient to target transmembrane proteins to either the axon or the dendrite through direct interactions with the clathrin-associated adaptor protein complexes (APs) in C. elegans. Axonal targeting requires AP-3, while dendritic targeting is mediated by AP-1. The axonal dileucine motif binds to AP-3 with higher efficiency than to AP-1. Both AP-3 and AP-1 are localized to the Golgi but occupy adjacent domains. We propose that AP-3 and AP-1 directly select transmembrane proteins and target them to axon and dendrite, respectively, by sorting them into distinct vesicle pools. •AP-3 and AP-1 sort transmembrane proteins to the axon and the dendrite, respectively•AP-3 strongly binds to axonal sorting motifs and select cargos to axonal vesicles•AP-3 and AP-1 are localized and functioning at different domains of Golgi apparatus Li et al. studied how axonal and dendritic proteins are targeted to their destined compartments from Golgi apparatus in C. elegans. AP-3 strongly binds to axonal sorting motifs and select cargos to the axon. Dendritic targeting is mediated by AP-1.