1. The New Zealand (NZ) sea lion Phocarctos hookeri is NZ's only endemic pinniped and is listed as 'nationally critical'. The species breeds in the NZ sub-Antarctic: 71% of the population at the Auckland Islands (2010 pup production: 1814 Ϯ 39) and the remaining 29% on Campbell Island (726 pups in 2010).
2.Pup production at the Auckland Islands has declined by 40% since 1998 (1998: 3021 pups produced): only 1501 pups were born in 2009. This decline is directly linked to philopatric females not returning to breeding areas. While the Auckland Island population has declined, the Campbell Island population appears to be increasing slowly. 3. Potential reasons for the decline in the Auckland Island population, but not in the Campbell Island population, include non-anthropogenic factors: (i) disease epizootics, (ii) predation, (iii) permanent dispersal or migration, (iv) environmental change; and anthropogenic impacts: (v) population 'overshoot', (vi) genetic effects, (vii) effects of contaminants, (viii) indirect effects of fisheries (i.e. resource competition) and (ix) direct effects of fisheries (i.e. by-catch deaths). Of the nine potential reasons examined here, six can be discounted (ii-vii). Bacterial epizootics (i) occur in the NZ sea lion population, but their impact has predominantly increased pup mortality, which is unlikely to cause the severe decline observed, as pup mortality throughout the species is naturally high and variable. 4. The most plausible hypotheses, based on available evidence, are that the observed decline, in particular, the decreasing number of breeding females in the Auckland Island population, is caused by (viii) fisheries-induced resource competition and (ix) fisheries-related by-catch. By-catch is the main known anthropogenic cause of mortality in the species. Competition with fisheries resulting in resource competition, nutrient stress and decreased reproductive ability in NZ sea lions should be a priority area for future research.