Based on phenotype and mode of action somatic mutations involved in stem colour of bamboo are possibly caused by transposon activity. The study of transposon activity and their possible relation to certain mutations is very difficult. In bamboo no breeding systems are available to detect transposon activity through classical breeding. Molecular approaches may provide some shortcuts, but to link the presence and activity of transposons to certain phenotypic markers is again a difficult task. A first approach to identify the molecular basis of these somatic mutations was to use primers based on sequence information from the 4.5 kb Ac9 transposon from maize. Several primer combinations were used and several copies with considerable homology to the original Ac9 transposons were present (Gielis and Sormann, 1997), which eventually turned out to be a useful and relatively cheap method to identify bamboos, at the species level.