Copepods are the most numerous animals and play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest numerical density, as the most cosmopolite copepod. The Oithona male paradox obliges it to alternate immobile and mobile phases for ambushed feeding and mate search respectively, while the female is less mobile and often feeding. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics and protein-protein interactions approaches. Tubulin-β3 and α immunofluorescence analysis revealed two lateral male-specific nervous ganglions in the first segment of the Oithona nana male’s prosome. In parallel, the transcriptomic analysis showed male-specific enrichment for nervous system development related transcripts. Twenty seven Lin12-Notch Repeat domains-containing proteins coding genes (LDPGs) over the 75 LDPGs found in the genome were specifically expressed in male. Furthermore, most of the LDPGs (27%) code for proteins having a predicted proteolytic activity and non-LDPGs proteolysis associated transcripts showed a male specific enrichment. Using yeast double–hybrid assays, we constructed a protein-protein interaction network involving two LDPs with proteases, extracellular matrix proteins and neurogenesis related proteins. In our study, the lateral nervous ganglion of O. nana male is described for the first time and is unique in copepods. We also demonstrated a role of the LDPGs and its associated proteolysis to participate to the male-specific physiology and we hypothesize a role of the LDPGs in the lateral ganglions development through guiding lysis of extracellular matrix for the neurites and synapse genesis.