The salmon louse (Lepeophtheirus salmonis) is an important pathogen in salmon aquaculture and a serious threat to wild populations of salmon. Knowledge of its basic biological processes such as reproduction is crucial for the control of this parasite and can facilitate development of a vaccine. Here, a novel yolk-associated protein, LsYAP, was characterised. Quantitative PCR and in situ analysis demonstrated that transcription of LsYAP takes place in the subcuticular tissue of adult females in the reproductive phase. LsYAP protein is transported and deposited in the developing eggs in the genital segment, where further processing takes place. The sequence characteristics, histological localisation and transcript regulation suggest that LsYAP is a yolk-associated protein. In addition, the use of RNA interference is, to our knowledge, demonstrated for the first time in a copepod. Treatment of adult females with double-stranded RNA led to lethality and deformations of offspring only. This result confirms that the LsYAP protein is produced in adult females but is utilised by the offspring.