The branching pattern of a plant directly affects its reproductive organs. For cut flowers of Chrysanthemum indicum hybrids flower size and stability of the shoot are important characteristics. The development of side shoots establishes new "sinks", which compete for nutrients and assimilates with the primary flower and primary stemreducing their size and persistence. To describe the diversity of these traits a collection of 78 European C. indicum hybrid varieties were phenotyped. Varieties with large flowers and only a few side shoots could be identified (e. g. FM). To analyse correlations between genetic relatedness and phenotype 448 AFLP-markers were used to compute similarity dendrograms based on the genetic diversity estimated by the Jaccard index and subsequent clustering by the Neighbour Joining method .To analyse the genetic architecture of shoot branching in Chrysanthemum the expression of candidate genes involved in schoot branching (Ls, MAX3 and MAX4) was analysed by semiquantitative PCR in strongly and weakliy branched varieties. However, the expression of these genes gave no explanations for the differences in the branching pattern found for these plants.The varieties were also screened for differences in the MAX4 gene by SSCP-markers via PAGE. One marker fragment had a significant impact on shoot branching. Plants sharing this fragment showed a mean decrease of 18% of side shoots compared to those without this fragment. By further investigation of genotypic differences of key factors controlling shoot branching useful molecular markers might be identified for C. indicum hybrids to select plants with reduced side shoot formation.