Here, we examine the synaptic function of the receptor protein tyrosine phosphatase (RPTP), Dlar, and an associated intracellular protein, Dliprin-alpha, at the Drosophila larval neuromuscular junction. We show that Dliprin-alpha and Dlar are required for normal synaptic morphology. We also find that synapse complexity is proportional to the amount of Dlar gene product, suggesting that Dlar activity determines synapse size. Ultrastructural analysis reveals that Dliprin-alpha and Dlar are required to define the size and shape of the presynaptic active zone. Accordingly, there is a concomitant decrease in synaptic transmission in both mutants. Finally, epistasis analysis indicates that Dliprin-alpha is required for Dlar's action at the synapse. These data suggest a model where Dliprin-alpha and Dlar cooperate to regulate the formation and/or maintenance of a network of presynaptic proteins.