Allozyme variation was examined in sockeye salmon (Oncorhynchus nerka) from 83 distinct spawning sites representing all major sockeye-producing river systems in Canada. Of 33 nonselected loci examined, only 14 were highly polymorphic (q > 0.05) and 10 were less polymorphic (0 < q ≤ 0.05). No two populations were fixed for different alleles at any locus, but allele frequencies ranged from 0.01 to 0.86 at PGM-1* and from 0.07 to 0.89 at ALAT*, the two most variable loci. Mean heterozygosity ranged from 2.3 to 5.6% (mean 4.1%) across all sites. Hierarchical analysis was used to partition relative gene diversity among river systems (6.3%), major drainages within a river system (2.9%), nursery lakes within drainages (7.0%), spawning sites within lakes (1.0%), and individuals within spawning sites (82.8%). Extensive differentiation among nursery lakes affords excellent opportunities for genetic stock identification within river systems, but the relatively weak regional structuring limits opportunities for coast-wide stock identification. Genetic variation at highly structured loci corroborates the view that modern populations in Canada originated from sockeye that survived the late Wisconsin Glaciation in the Bering and Columbia refuges, and also suggests the existence of coastal refuges in British Columbia.

A persistent period of low abundance in what was once the second largest fishery for sockeye salmon Oncorhynchus nerka in British Columbia has kept the Rivers Inlet fishery closed since 1996. Initial speculation about the cause of the decline focused on factors such as reduced egg‐to‐fry survival, declining quantity and quality of spawning habitat, and reduced fry‐to‐smolt survival in Owikeno Lake (the only nursery lake in Rivers Inlet). We developed an index of juvenile sockeye salmon abundance by combining direct estimates of abundance from trawl surveys with indirect estimates of abundance inferred from density‐dependent growth of juvenile sockeye salmon. Juvenile growth data were available as either direct samples of presmolt weight or as measurements of freshwater growth from the scales of returning adults. Collectively, these data do not indicate a long‐term decline in juvenile sockeye salmon abundance since the 1950s. Throughout the 1970s and 1980s and even more recently (1991 and 1994 brood years), the juvenile abundance index exceeded the long‐term mean. If freshwater abundance was either untrended or increasing, the most likely cause of the population decline would have been lower survival after the fry stage, which would have been noticeable in the 1970s and especially from 1992 to 1998. Poor marine survival is the most parsimonious explanation for the declining fry‐to‐adult survival in Owikeno Lake, particularly in light of coincident declines in sockeye salmon returns per spawner at Long Lake (a nearby pristine watershed) and declines in adult sockeye salmon abundance in other populations to the north of Rivers Inlet.

We demonstrate the present analytical capability and the potential for coast-wide stock identification of sockeye salmon (Oncorhynchus nerka) using reference sampling data from 51 principal stocks in British Columbia and Southeast Alaska situated between the Fraser and Taku Rivers. We evaluate the relative accuracy and precision of stock composition estimates from maximum likelihood mixture analysis with four types of biological markers, either alone or in combination; these include freshwater age, six scale pattern variables, the prevalence of the brain parasite Myxobolus neurobius, and five biochemical genetic (electrophoretic) traits. Using all markers in combination, estimates of mixing proportions for all test mixtures are acceptable for most purposes (roughly ± 10% with 95% confidence) providing all samples are representative and mixture samples are large ([Formula: see text] fish). The reliability of these estimates is greatly reduced when reference samples are corrupted to simulate observed annual variation in scale pattern markers. Annual variation may preclude the use of scale pattern markers for complicated stock identification problems where representative reference samples cannot be obtained annually, or until after the fishing period. In contrast, no significant annual variation is detectable for biochemical genetic and brain parasite markers in stocks that have been sampled repeatedly. Using only these stable markers, contributions from about 15 different groups of the 51 stocks can be estimated with acceptable precision, but in general, estimates for individual stocks are unreliable.

The genetic influence of stocking on the Atlantic salmon (Salmo salar) population from the Spanish Esva River was analysed by electrophoresis of protein loci. Genetic variation within parr and mature male parr samples demonstrated that Scottish-origin parr stocked in 1990 survived the first summer. However, samples collected from returning adults in 1990 and 1991 did not indicate any contribution from previous stocking programs. Altered MEP-2* frequencies indicate that the native gene pool may have been disrupted by foreign genomes from precocious males or grilse.

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