ML superfamily represents a group of proteins playing important roles in lipid metabolism and innateimmune response. In this study, we report the identification of the first component of the ML superfamilyin the invertebrate Ciona intestinalis by means of a subtractive hybridization strategy. Sequencehomology and phylogenetic analysis showed that this protein forms a specific clade with vertebratecomponents of the Niemann-Pick type C2 protein and, for this reason, it has been named Ci-NPC2. Theputative Ci-NPC2 is a 150 amino acids long protein with a short signal peptide, seven cysteine residues,three putative lipid binding site and a three-dimensional model showing a characteristic b-strandstructure. Gene expression analysis demonstrated that the Ci-NPC2 protein is positively upregulated afterLPS inoculum with a peak of expression 1 h after challenge. Finally, in-situ hybridization demonstratedthat the Ci-NPC2 protein is preferentially expressed in hemocytes inside the vessel lumen.