| Summary: | <i>Saprolegnia parasitica</i> is recognized as one of the most important oomycetes pests of salmon and trout species. The amplified fragment length polymorphism (AFLP) and method sequence data of the internal transcribed spacer (ITS) were used to study the genetic diversity and relationships of <i>Saprolegnia</i> spp. collected from Canada, Chile, Japan, Norway and Scotland. AFLP analysis of 37 <i>Saprolegnia</i> spp. isolates using six primer combinations gave a total of 163 clear polymorphic bands. Bayesian cluster analysis using genetic similarity divided the isolates into three main groups, suggesting that there are genetic relationships among the isolates. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCO) confirmed the pattern of the cluster analyses. ITS analyses of 48 <i>Saprolegnia</i> sequences resulted in five well-defined clades. Analysis of molecular variance (AMOVA) revealed greater variation within countries (91.01%) than among countries (8.99%). We were able to distinguish the <i>Saprolegnia</i> isolates according to their species, ability to produce oogonia with and without long spines on the cysts and their ability to or not to cause mortality in salmonids. AFLP markers and ITS sequencing data obtained in the study, were found to be an efficient tool to characterize the genetic diversity and relationships of <i>Saprolegnia</i> spp. The comparison of AFLP analysis and ITS sequence data using the Mantel test showed a very high and significant correlation (<i>r</i><sup>2</sup> = 0.8317).
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