Sea lice are copepod ectoparasites of major importance in salmonid aquaculture. Under controlled challenge testing, individual lice count has moderate heritability and has been suggested as a trait in genetic selection for parasite control, under the assumption that selection for reduced individual parasite burden provides group-level protection against the parasite. Recent studies indicate that genetic variation of lice count in Atlantic salmon is mostly explained by variation in initial infestation, rather than ability to limit parasite burden after infestation. Results from a selection experiment are presented, with two Atlantic salmon (Salmo salar) lines divergently selected for low/high parasite burden, showing substantial between-strain difference under common-garden testing. An experiment was performed where the final generation of the divergently selected salmon lines were challenge tested separately to assess potential for group-level protection against sea lice. The results showed that, despite the two groups being clearly different under common garden testing, the line difference was not significant when tested separately, i.e., no evidence for group-level protection. However, in a follow-up experiment, using a more realistic lice challenge model under water-flow, expected to be less favorable for the parasite, significant group-level differences were found, albeit smaller than under common garden testing. The results show that the potential for group-level protection is lower than suggested by within-group genetic variation in lice count, and more so for environments giving the parasites easy access to hosts. These results cast some doubt about the efficacy of selective breeding for reduced lice count as a tool for group-level parasite control in densely populated fish farm environments.