The minke whale (Balaenoptera acutorostrata) is a globally-distributed species whose population ecology is poorly understood. Most knowledge about minke whale populations, including gender differences, originates from historical data collected during commercial harvests. Here we present results from an investigation of the population structure of minke whales along the north shore of the Gulf of St. Lawrence in Québec, Canada. Our methods involved the review of 5,000 photographs and the genetic analysis of 196 skin biopsies from individual minke whales encountered during the summers of 2007-2015. To maximize individual recognition reliability, we analyzed photographs of whales with 2+ notches in the dorsal fin, or with dorsals exhibiting unique scarring and/or deformation. Results demonstrated variation in annual marking rates of 8%-13%, with intra-annual recaptures of individuals spanning up to 104 days. Twelve individuals were recaptured in multiple years, and one whale was recaptured in 6 years. Despite a limited sample size (n=35), the proportion of whales recaptured suggests some site-fidelity in the study area. Results from biopsy analyses using 20 microsatellites indicated 6 intra- and 10 inter-annual recaptures. One recapture between 3 pairs of consecutive years was not sufficient for an abundance estimate yet this low number suggests a conservative population estimate of 200+ whales in the region. Moreover, 155 of 180 (86%) individuals were female. No calves were observed during the study period, suggesting that they wean before summer or that lactating females segregate from other females. Our collective results support whaling data indicating that minke whales may be the only rorqual (Balaenopteridae) exhibiting sex segregation during summer. Broader impacts of this research include the contribution of new information about gender-based site fidelity in minke whales visiting seasonal feeding areas and pose new questions about the reproductive role of the prey-rich Gulf of St. Lawrence in north Atlantic minke whale populations.