Atlantic herring (Clupea harengus) has complex population structure and dynamics including diverse life histories and spawning times with spring and autumn spawning as the most common modes. Originally, spawning herring were phenotypically identified based on their maturity development or otolith microstructure by determining seasonal specific larval growth patterns. Recently, genetic markers have revealed clear genetic differentiation between spring- and autumn-spawning populations. All three methods were applied to herring caught at the same locations during spring and autumn to determine the coherence of methods. In a selected subset, most herring (∼77%) had an otolith microstructure and genetic assignment coinciding with the phenotypically assigned spawning season. Non-spawning herring (>5%) that were classified as belonging to the current spawning season using genotyping and otolith-typing were assigned as skipped spawners. For ∼8% of spawning herring, the genetic and otolith assignment contradicted the phenotypically assigned spawning season, characteristic of straying individuals. Otolith-typing contradicted the genetic and phenotypical assignment in ∼7% of the cases, potentially representing individuals reuniting back to the spawning season favoured by their genotype. Although the viability of offspring from these individuals remains undocumented, it is suggested that the observed switching of spawning season may contribute to gene flow between herring populations.