Chemical synapses are fundamental units of neural communication. While the function of synapses has been extensively characterized, development and structural organization of synapses is poorly understood. In my thesis work, I have explored the molecular mechanisms of presynaptic development in C. elegans. I found that presynaptic assembly is hierarchically organized into three layers. In the first layer, presynaptic assembly is initiated by SYG-1/Neph, a transmembrane protein that is recruited to the synaptic site by direct interaction with SYG-2/Nephrin, which is also a transmembrane protein that serves as an extracellular instructive cue. Through unknown mechanisms, SYG-1 recruits SYD-2/Liprin-alpha and SYD-1, two key scaffold molecules that are critical for synapse formation and constitute the second layer in the synaptic hierarchy. In absence of syd-1 or syd-2/Liprin-alpha mutants, numerous synaptic components including synaptic vesicles fail to assemble at presynaptic sites. SYD-2/Liprin-alpha is a highly conserved coiled-coil domains containing component of the active zone that interacts with and therefore likely directly recruits multiple other active zone components including UNC-10/Rim, ERC/ELKS-1, and GIT. These active zone components, along with numerous other synaptic components such as synaptic vesicles, synapsin, endophillin, and calcium channel subunits that depend on SYD-2/Liprin-alpha for localizing to presynaptic sites form the third synaptic layer. Proteins in this third layer, which although might play an important functional role in the synaptic vesicle cycle, are largely dispensable for synapse formation. I found genetic and biochemical evidence that SYD-1 is a positive regulator of SYD-2/Liprin-alpha function that facilitates interaction of SYD-2/Liprin-alpha with its binding partners such as ELKS-l. I also discovered RSY-1, a novel negative regulator of presynaptic assembly that counteracts prosynaptogenic activity of SYD-1 by inhibiting SYD-1 and SYD-2/Liprin-alpha function. Interaction between SYD-1 or SYD-2/Liprin-alpha and ELKS-1 is weakened in the presence of RSY-1. Loss of RSY-1 leads to increased accumulation of synaptic material and a partial failure in synapse elimination. Taken together, presynaptic assembly is dependent on a key scaffold molecule SYD-2/Liprin-alpha whose activity is tightly regulated by both positive and negative factors.