This is a review of genetic mapping with molecular markers aimed at the non-specialist who wishes to use, or at least grasp the concepts behind, this powerful analytical tool. Restriction fragment length polymorphisms (RFLPs) are defined and used to illustrate the different aspects of mapping. The principles of segregation, recombination and linkage are considered and related to the idea of a molecular marker map. A description of a typical mapping population and how it is analysed follows. Traits to be mapped are divided into those controlled by ‘major’ genes and those governed by quantitative trait loci (QTLs). Exploitation of the map for marker-assisted selection, gene cloning and synteny comparisons is discussed, as are some of the limitations to the usefulness of molecular marker maps. Finally other marker systems are introduced, namely minisatellites or variable number tandem repeats (VNTRs); randomly amplified polymorphic DNA (RAPDs); microsatellites or simple sequence repeats (SSRs); and amplified fragment length polymorphisms (AFLPs).