The salmon louse Lepeophtheirus salmonis is a challenging ectoparasite for the salmon farming industry and wild salmonids. Salmon lice have a very high reproductive output, that require deposition of large amounts of lipids into growing oocytes as a major energy source, most probably mediated by lipoproteins. Microsomal triglyceride transfer protein (MTP) is essential for the assembly of lipoproteins. Salmon lice have three LsMTP transcript variants encoding two different protein isoforms predicted to contain three β sheets (N, C and A) and a central helical domain, similar to MTP from other species. In adult females, LsMTP is transcribed in sub-cuticular tissues, intestine, ovary and mature eggs, but differently for the three variants, and quantitatively different at various developmental stages. LsMTP RNAi knockdown in females produced offspring with significantly less neutral lipids in their yolk and only 10-30% survival. The present study suggests the importance of LsMTP in the reproduction and lipid metabolism in adult female L. salmonis, a possible metabolic bottleneck that could be exploited for the development of new anti-parasitic treatment methods.