Summary Public concerns about the issue of the environmental safety of genetically modified plants have led to a demand for technologies allowing the production of transgenic plants without selectable (antibiotic resistance) markers. We describe the development of an effective transformation system for generating such marker‐free transgenic plants, without the need for repeated transformation or sexual crossing. This system combines an inducible site‐specific recombinase for the precise elimination of undesired, introduced DNA sequences with a bifunctional selectable marker gene used for the initial positive selection of transgenic tissue and subsequent negative selection for fully marker‐free plants. The described system can be generally applied to existing transformation protocols, and was tested in strawberry using a model vector in which site‐specific recombination leads to a functional combination of a cauliflower mosaic virus 35S promoter and a GUS encoding sequence, thereby enabling the histochemical monitoring of recombination events. Fully marker‐free transgenic strawberry plants were obtained following two different selection/regeneration strategies.