Microseris douglasii (DC.) Sch.-Bip. and M. bigelovii (Gray) Sch.-Bip. are two small annual autogamous species of Compositae with nearly non-overlapping distribution ranges in Western North America. Specifically, M. bigelovii occurs directly along the Pacific coast, whilst M. douglasii has an inland distribution including patches of serpentine soil. Both species are variable, and artificial hybrids between them vary widely in fertility depending on the individual parents. Segregating offspring of one hybrid (strain H27) is being used to analyse the genetic basis of characters differentiating the two species by QTL mapping with RAPDS and ALFPs as molecular markers. Technical problems with mapping dominant markers in a wide cross will be briefly listed and QTL analysis will be discussed. For the genetic analysis of physiological characters, the precise definition of the characters is crucial and the methods of scoring or measuring phenotypes in different environments eventually require more time and effort than the molecular characterization. We are establishing recombinant inbred lines to provide material for more complex physiological analyses requiring several plants per genotype. An increasing number of characters is being studied in this cross, and the possibility of shared pleiotropic QTLs is high. The potential number of QTL genotypes by far exceeds the number of actual genotypes in these lines. We are characterizing the gene interactions as closely as possible and making quantitative genetic models to predict the genotypes corresponding to all possible genotypes. These predictions are converted via computer modelling into an increasingly realistic three-dimensional representation of the growing plant useful for a simulation of plant evolution.