Sea lice, especially Lepeophtheirus salmonis and Caligus spp., have the greatest economic impact of any parasite in salmonid fish farming and are also a threat to wild salmonids. Here, I review how the biology and ecology of various louse and host species influence their pathogenicity and epidemiology. Recent discoveries of new species and genotypes emphasize the need for more basic research on louse taxonomy and host preferences. Louse development rates are strongly dependent on temperature, and increasing mean sea temperatures are likely to increase infestation pressure on farms and wild fish, as well as affecting the geographical distribution of hosts and parasites. Despite progress in finding L. salmonis larvae in the plankton and in modelling louse production in several countries, more data on larval behaviour and distribution are required to develop dispersal and transmission models for both L. salmonis and Caligus spp. This knowledge could be used to take measures to reduce the risks of lice affecting farmed and wild fish.