Five microsatellite loci were used to examine genetic variation within and among putative populations of the eulachon, Thaleichthys pacificus (Pisces: Osmeridae), over the entire range of the species. A previous mitochondrial DNA study, while revealing a high degree of genetic variation within the species, did not resolve the level of population sub-division expected for this anadromous fish. Two microsatellite loci were developed from eulachon DNA and, in addition to three microsatellite loci from the rainbow smelt, Osmerus mordax, were employed as a class of "higher resolution" markers in an attempt to further resolve the population structure of eulachon. The level of genetic variation observed at these loci was surprisingly low (heterozygosity ranged from 4% to 64%; number of alleles ranged from three to ten; maximum size range of alleles was 16 base pairs), yet revealed the greater power of microsatellites over mitochondrial DNA for resolving population sub-division within eulachon. More pairwise population comparisons were significant with the microsatellite data, and the microsatellite F ST value was twice the value observed with mtDNA (mtDNA F ST=0.023; microsatellite F ST=0.045). Despite this greater sensitivity, it was difficult to define distinct demographic units in eulachon, a species which is currently the focus of conservation concern. Eulachon highlight the challenges of examining population structure in species with inferred high gene flow.