While Atlantic salmon (Salmo salar L.) spawn in late autumn/early winter, their return migration to freshwater from the sea can occur at any time during the year. The diversity in the run timing of Atlantic salmon (defined as the time of return of adults to rivers from the sea) is of great significance to fisheries, as it results in fresh-run fish being spread out through the year, increasing the temporal extent of the catching period. In order to maintain the wide diversity observed in salmon fisheries, it is important to maintain the diversity of the populations that underpin them. Recently, a number of genetic markers associated with run timing were identified which raised the possibility of developing these into a tool that could be used to screen juvenile salmon and characterise stocks according to their run timing composition. Here, we describe the development and calibration of a panel of twelve genetic markers that could be used as a tool to determine run timing proportions in juvenile Atlantic salmon.