Several species in the noctuid genus Xestia exhibit periodic dynamics, with two coexisting cohorts flying in alternate years. The population dynamics and two-year life cycle of Xestia moths suggest that the two cohorts are more or less isolated in time. Typically one cohort is abundant and the other one is rare. Knowledge of the extent of isolation between the two cohorts is important to fully understand the population dynamics and the evolution of alternate-year flight in these species. We applied allozyme electrophoresis and mitochondrial genome sequencing to infer the extent of genetic differentiation among different cohorts of Xestia tecta (Hübner) within the same geographical area as well as between cohorts with opposite-phase flight pattern in different geographical regions. We found no evidence for substantial genetic differentiation and isolation between the even- and odd-year cohorts in eastern Lapland, nor between the cohorts in eastern and western Lapland. The most informative markers were the most polymorphic allozyme loci (Pgm and Mpi) and the AT-rich region in the mtDNA. However, owing to the generally low levels of genetic variation it was not possible to establish conclusively the degree of genetic isolation between the different cohorts. We discuss the implications of our results in relation to two different hypotheses which could account for this pattern: ongoing gene flow between different cohorts and recent common ancestry.