Scotch broom, Cytisus scoparius, spreads rapidly in parts of Denmark and is considered an invasive species by some authors. However, the species has been present in the Danish flora for centuries and is therefore considered native to Denmark. In the present study we explore whether Danish Scotch broom consists of one or two gene pools with potential differences in phenotype and invasiveness. One plastid and five nuclear microsatellite markers were used to reveal potential substructuring of Danish Scotch broom. Nine populations were included representing populations exhibiting invasive behaviour and populations showing non-invasive behaviour. An Italian population was used as reference. Bayesian analysis based on genetic markers indicated that the sampled populations form two distinct gene pools, and this pattern was supported by neighbour-joining trees. Measurements of height and width of the analysed plants showed that the two gene pools correspond to populations exhibiting either a horizontal habit and non-invasive behaviour or an erect habit and, in some cases, invasive behaviour. The Italian population clustered with the erect ones. We discuss the origin and taxonomic status of the two gene pools and conclude that Danish horizontal Scotch broom should be given a formal taxonomic status in order to initiate conservation activities for its protection.