Recent advances in cytogenetics of the Lolium/Festuca complex provide new opportunities for understanding and manipulating physiological mechanisms in complex quantitative traits such as stress resistance. The complex provides a valuable reserve for research and breeding since (a) it includes a wide range of valuable agronomic characters, (b) it has the capacity for intergeneric hybridization with promiscuous recombination, and (c) its genomes, despite their close homology, have sufficient structural heterogeneity to allow Lolium and Festuca chromosomes to be discriminated using genomic in situ hybridization (GISH). Two alternative procedures are used to ‘dissect’ stress-resistance traits into their individual components both to determine their function and to physically map the relevant QTL(s) onto chromosome arms: (a) Festuca genes are introgressed into Lolium to improve stress resistance, (b) Lolium genes are introgressed into Festuca to reduce stress resistance. Whichever approach is used, alien introgressions can be detected by GISH and assigned to chromosome arms to create a physical map. Genes of interest may then be located more accurately following further recombination events which reduce the size of the relevant alien introgression. It has become obvious during the past years that genetic and physical maps are not directly comparable as chiasmata are not evenly distributed along the chromosome axis. By integrating physical maps created by GISH and genetic linkage-maps, the precise site of genes on a chromosome arm may be determined, and markers found which are tightly linked to the genes of interest, for future use in breeding programmes.