The molecular structure and role of two splice-isoforms of Unc-5 (Hp-Unc-5v1 and v2) in Unc-5/netrin interaction during serotonergic axonal projection were elucidated in this study. Hp-Unc-5v1 was found to be comprised of two immunoglobulin-like domains, two thrombospondin domains in the extracellular region, and ZU-5, DB, and Death domains in the cytoplasmic region, whereas Hp-Unc-5v2 lacked one thrombospondin domain, the transmembrane domain, and all cytoplasmic domains. Hp-Unc-5v1 was transcribed in unfertilized eggs, which continued until the 3-day post-fertilization (-dpf) 2-arm pluteus stage, but was suspended at the mesenchyme blastula stage (mB1), whereas Hp-Unc-5v2 was not transcribed in unfertilized eggs, but was from after fertilization to the same developmental stage of mB1 as Hp-Unc-5v1. Relative accumulation of transcripts of both splice-isoforms peaked at the prism stage and declined thereafter, and they were localized at the vegetal pole region of early gastrulae, around the blastopore in mid- to late gastrulae, at fore- and mid-gut regions and on the basal side of dorsal ectoderm in 28-hour post-fertilization prism larvae, and within axons at and after the 2-dpf pluteus stage. Hp-Unc-5v2:GFP was detected in the entire serotonergic cell body and extracellularly on the basal surface of oral ectoderm in 2-dpf plutei and exclusively within axons in 4-dpf plutei. Overexpression of Hp-Unc-5v2 resulted in decreased axonal projection in plutei. Knockdown of Hp-Unc-5v1 by morpholino antisense oligonucleotide resulted in severe deficiency of axonal projection. Interference of Unc-5/netrin interaction using an exogenous synthetic SQDFGKTW peptide from the VI domain in Hp-netrin inhibited axonal projection and larval swimming.