DNA markers have been used in many studies of fungal plant pathogens, and in particular in investigations of mating systems, gene flow, the establishment of epidemics and adaptation to host crops. Many aspects of population structure can be analysed by means of contingency tables, using χ2 tests. Some extensions of such tests, with particular applications to plant pathology, are described. One test is applicable to situations where there is more than one level of subdivision of populations, while another is appropriate when there are two types of division, for instance by geographical area and by host crop. Furthermore, the χ2 test offers a convenient way of combining information from several independent markers. Tests for the differentiation of subpopulations are based on certain underlying assumptions, and it is argued that the primary consideration in choosing a marker system should be whether or not it fits the appropriate genetic criteria. Other considerations, such as time, cost and difficulty, should be evaluated if two or more methods are capable of generating markers which fit the genetic assumptions adequately. Although a large number of markers should be examined in order to estimate the extent of population subdivision, it might only be necessary to use a few markers to test whether such subdivision exists. Likewise, only a few markers may be needed to distinguish clones of a pathogen in a partially sexual population. However, in all of these tests, these markers should be well characterized genetically. It is shown that an existing genetic fingerprinting system for the barley powdery mildew fungus, Erysiphe graminis f. sp. hordei, is suitable for identifying clones but not for describing the differentiation of subpopulations. It may be possible to use markers based on random amplified polymorphic DNA (RAPD) or on amplified fragment length polymorphism (AFLP) in quantitative research in population genetics of E. graminis f. sp. hordei.