SYD-2, the C. elegans homolog of Liprin-alpha, is a synapse active zone protein that affects distribution of synaptic vesicle proteins (SVps) and lysosomal proteins in neurons. We show that SYD-2 affects SVp trafficking, such that the composition of SVp carriers is altered. We have previously shown that LRK-1, the C. elegans homolog of the Parkinson's protein LRRK2, acts through the AP-3 clathrin adaptor complex to affect SVp trafficking and SVp carrier composition. Additionally, both LRRK2 and the AP-3 complex are known to affect lysosomal protein trafficking. Therefore, using
syd-2 mutants, we set out to test if there are common genetic regulators for trafficking of SVp and lysosomal proteins. We show that
lrk-1 and
apb-3 likely act upstream of
syd-2 to exclude lysosomal proteins from SVp carriers in the cell body, suggesting that separation of SVps and lysosomal proteins is a necessary step in SVp carrier biogenesis. Furthermore, we show that lysosomal proteins mislocalize to the neuronal process in
syd-2,
lrk-1 and
apb-3 mutants, unlike in wildtype where they are restricted to the cell body. The axonal mislocalization of lysosomal proteins in the
syd-2 mutant is dependent on the AP-3 complex and independent of LRK-1, suggesting that SYD-2 acts together with AP-3 complex to retain lysosomal proteins in the cell body. Altered SVp carriers formed in
lrk-1 and
apb-3 mutants mislocalize to the dendrites via the AP-1 clathrin adaptor complex. We show that SYD-2 genetically interacts with the AP-1 complex to prevent the mis-formed SVp carriers from entering dendrites. These data suggest that SYD-2 interacts with two distinct clathrin adaptor complexes to regulate polarised distribution of SVps and lysosomal proteins. Additionally, our data suggest that early trafficking of SVps and lysosomal proteins is linked and is regulated by common genetic factors.