A knowledge of genetic structure in natural populations is often neces
sary for conservation and management purposes, especially in declining
Pacific salmon populations. To test for genetic differentiation betwe
en nine populations of chinook salmon, Oncorhynchus tshawytscha, from
south-western British Columbia, Canada, DNA was extracted from 603 fis
h and hybridized with a single-locus minisatellite probe. Multivariate
statistical analyses of the resulting allele size data permitted succ
essful overall population identification of 52% (individual population
range: 24-78%; P < 0.005), indicating a high level of genetic differe
ntiation among the nine populations. Two of the nine populations were
further analysed using data from a second minisatellite locus. The dis
crimination success rate improved from 81.1% (one-locus analyses) to 9
0.0% (two-locus analyses), indicating the potential for greatly increa
sed resolution gained by the addition of more loci. These results indi
cate that variation at minisatellite loci can be used for assessing po
pulation-level genetic structure, even with artificial gene flow.