Amplified Fragment Length Polymorphism (AFLP) analysis has been used to analyse 100 Australian, European and North American
isolates of Leptosphaeria maculans. All isolates had distinct AFLP profiles. They could be classified into five types, which had very few
AFLP bands in common and corresponded to classifications made previously on the basis of ability to cause stem cankers on Brassica
napus (A group), or inability to do so (B group), and on host range. Four isolates had AFLP profiles completely dissimilar to these
groups and to each other. Genetic diversity and geographic differentiation were analysed separately within AFLP types 1 and 2.
UPGMA analysis of the 66 AFLP type 1 (A group) isolates using 50 polymorphic bands did not provide evidence for clustering
according to geographic origin. Non-metric multidimensional scaling (NMDS) analysis suggested that the Australian and European
populations were separate adjacent clusters, while the North American population partially overlapped both the others. This
geographic differentiation was supported by Wright's fixation index (Fst) analysis. Three measures of genetic variability between
isolates within regions (effective number of alleles, gene diversity, and Shannon index) showed that the North American A group
isolates were less diverse than those from Australia and Europe. The 21 AFLP type 2 (B group; NA1 sub-group) isolates did not
cluster based on geographic region, which was confirmed by NMDS and Fst analysis. There was a similar degree of genetic diversity
within A group and the NA1 sub-group of B group isolates. Unlike other techniques, AFLP analysis can readily discriminate
between group B isolates of the L. maculans complex that were previously difficult to classify and also provides individual
fingerprints for isolates. Isolates of the A group and of the NA1 sub-group of B group could be also distinguished readily by
electrophoretic karyotyping, as the latter isolates had more bands smaller than 1.4 Mb than the A group isolates.