A genetic map is a valuable genetic tool, which can be used e.g. for QTL mapping. We have constructed a genetic map using microsatellites and gene-based markers with a special emphasis on genes related to flowering time (H. Kuittinen, J. Leppälä). We used sequence information from A. thaliana for PCR primer development. This is possible due to the short time since the taxa separated. Mapping genes in A. lyrata that are orthologous to genes in A. thaliana enables comparison of the genetic maps of the two species: distances between markers and to what degree there has been rearrangements in the chromosomes. If there is a high degree of colinearity, the information from a model species can be readily used in A. lyrata. The current map consists of 72 loci. As expected based on the close relationship between A. lyrata and A. thaliana, their maps show a high degree of colinearity. The map was constructed in the F2 progeny between two populations. This work involves a wide international collaboration (C.H. Langley, T. Mitchell-Olds).