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A comparison of the virulence, saprophytic growth, and genomes of 12 isolates of <i>Ilyonectria mors-panacis</i> and 4 isolates of <i>I. robusta</i> from Canada pathogenic to <i>Panax quinquefolius</i> was made. There were no significant differences in the average lesion size on detached roots between isolates of the two <i>Ilyonectria</i> species or isolates that originated from infected roots in first- or second-crop ginseng soils. This did not support the hypotheses that <i>I. mors-panacis</i> is always more virulent than <i>I. robusta</i> or that there is selection for higher virulence during the first crop. However, the average growth rate on potato dextrose agar for <i>I. robusta</i> was significantly greater than that of <i>I. mors-panacis</i>, and the average total genome size of <i>I. robusta</i> isolates was significantly smaller with a significantly higher GC content. On dendrograms based on nucleotide sequences of all predicted exons of the genomes, <i>I. robusta</i> isolates were distinguishable from <i>I. mors-panacis</i> isolates, which were similar but could be separated into types 1 and 2. The difference between type 1 and type 2 <i>I. mors-panacis</i> was not related to geographical origin, virulence, growth rate, or mating type. However, the division was also observed for the total predicted secretome, most notably small secreted cysteine-rich proteins and secreted proteases, indicating that type 1 and 2 isolates of <i>I. mors-panacis</i> may interact differently with their environment.