Cell adhesion molecules of the Immunoglobulin superfamily (IgCAMs) play diverse functions during neural development. Previously, we have identified SYG-1/Neph1 and SYG-2/Nephrin, IgCAMs necessary for synaptic specificity in Caenorhabditis elegans. Here, we conduct an in vivo structure-function analysis of SYG-1 and SYG-2 to identify domains of SYG-1 and SYG-2 necessary for heterophilic binding as well as synaptic specificity. We find the first Ig domain of SYG-1 and the first 5 Ig domains of SYG-2 are necessary and sufficient for their binding in vivo, as well as for synapse formation. We also find the SYG-2 cytoplasmic domain is required for SYG-2 subcellular trafficking, while the intracellular region of SYG-1 is required for synaptic function at earlier developmental stages, but is dispensable for later stages. This study defines the domain requirements for SYG-1/SYG-2 heterophilic binding and suggests that unknown SYG-1 extracellular interactors may play a role in SYG-1-mediated synaptic specificity.