Many fish species that are separated into genetically distinct populations are exploited as mixed stocks and this creates challenges for a sustainable management. European whitefish in the Baltic Sea represents one of these species forming sea- and river-spawning ecotypes, which are further divided into local populations. This study evaluated the effect of combining genetic markers with an adaptive meristic trait (gill-raker count, GRC) on the performance of mixed-stock analysis (MSA) of Baltic whitefish. Using 586 individuals from 13 spawning locations, a simulated mixtures analysis showed that the combination of GRC and nine microsatellites improves both the accuracy and precision of MSA for distinguishing two sympatric ecotypes. When applied to gill-net fishery samples (758 fish) collected around the Åland Islands, the estimated stock composition showed a large temporal shift in abundance of two ecotypes between June and November, with decreasing frequency of river spawners in autumn. Our results indicate that combining neutral genetic markers with the adaptive meristic trait provides a useful fisheries monitoring tool for conservation and management of two sympatric whitefish ecotypes in the Baltic Sea.