Lake sturgeon populations show a variety of movement patterns, but this variation is poorly understood. To compare two migratory phenotypes of lake sturgeon in the St. Clair River, multiple data types were analyzed. Individual fish were classified into migratory phenotypes based on acoustic telemetry data from 2012-2015. Lake sturgeon consistently showed movement from the St. Clair River upriver into Lake Huron or downriver into Lake St. Clair. The two migratory phenotypes were then compared for differences in morphometrics, genetics, and epigenetics. Morphological differences based on linear measurements were not detected between phenotypes. Microsatellite data from 11 loci suggested one population with no genetic differentiation between migratory phenotypes. Our epigenetic results indicated that the migratory phenotypes are differentially methylated (P=0.036), thus epigenetics may be associated with migratory differences in lake sturgeon. Only one restriction site was identified to be driving the differential methylation (P=0.012). While little evidence at neutral loci occurred for genetic differentiation of lake sturgeon, DNA methylation may play a role in the observed movement pattern variation. When combined with microsatellite and morphometric analyses, our results suggested that different migratory patterns may reflect phenotypic plasticity, allowing lake sturgeon to acclimate to short-term environmental variability. Without an integrated approach, the role of epigenetics in the migratory phenotype of lake sturgeon may have been overlooked. Further characterization of migratory phenotypes could be important for management to conserve behavioral variation across the distribution of lake sturgeon and for design of stocking guidelines.