Little is known about the population structure of Alaskan rockfishes, including Pacific ocean perch (POP, Sebastes alutus), and how persistent and variable oceanographic features may influence their structures. Moreover, early life history information is sparse for many species. We used data from 14 microsatellite loci to characterize the genetic structure of young-of-the-year Pacific ocean perch collected during 1998–2003 from the Gulf of Alaska and Bering Sea. Broad-scale geographic variation in genetic structure of the young-of-the-year (FST = 0.005, P < 10−4) had similarities to that observed in a previous adult study. The overall correlation between genetic and geographic distance (isolation by distance) was nearly identical to that observed in the adults. Fine-scale geographic divergence was also observed and may be the result of oceanographic circulation features within the Gulf of Alaska. Interannual variation (between cohorts) at locations sampled in more than one year is consistent with variable oceanography and fine-scale population structure rather than the influence of a sweepstakes effect. The similarities of the young-of-the-year with the adults and the pattern of genetic divergence confirm that dispersal of Pacific ocean perch is limited in all life stages.