We examined the genetic structure of the threatened spectacled eider 14–18 years after the initial assessment to evaluate the influence of population recovery on diversity. Concordant with the initial assessment, spectacled eiders were highly structured at mitochondrial (mt) DNA and lacked differentiation at microsatellite loci. The degree and spatial pattern of structure has changed at mtDNA; a 33.0–40.3% reduction in overall FST and ΦST, respectively, and a marked reduction in pairwise FST (-83.1 to -91.4%) among Alaska sites. Reduction in genetic structure is suggestive of increased female dispersal within Alaska. These findings highlight the importance of reevaluating genetic diversity as species recover from declines as microevolutionary and demographic processes are dynamic and continually shape associations among populations.