Recently, a genetic tool has been developed that characterises the different run timing components in Atlantic salmon, more specifically the early run. Here, we apply this tool to estimate the early running component of juvenile Atlantic salmon caught in nine rivers, eight rivers along the northeast coast of Scotland and one along the west coast. The estimated early run timing proportion for each site was mapped to gain information on within and between-river patterns. These maps can be used to inform river managers of the areas with a large early running component and may help achieve their conservation aims.