The Australian Phoma rabiei population was previously found to be genetically narrow with only one mating type gene detected, potentially precluding evolution through recombination. However, a diverse range of aggressiveness has been detected, some able to cause severe disease on elite cultivars. To better understand the risk to currently used resistance sources through selective adaptation, a total of 416 isolates were hierarchically collected from within all major Australian chickpea growing regions and from commonly grown cultivars in 2013 and 2014. Genotyping via SSR loci indicated an overall low diversity (0.074), as previously observed. Although a large number of haplotypes were detected (78), more than 64% of the population belonged to a single dominant haplotype (ARH01). Pathogenic screening on a differential host set, revealed distinct isolate pathotype groups, with 17% of all isolates assessed identified as highly aggressive. Of these, over 60% were of the ARH01 haplotype. A similar pattern was observed at the host level, with 46% of all isolates collected from Genesis090(R) identified as highly aggressive, of which 50% were of the ARH01 haplotype. This is very high compared to the percentage of aggressive isolates detected within other haplotype groups and indicates that the ARH01 haplotype is not only widely adapted to the diverse agrogeographical environments of the Australian chickpea growing regions, but contains a disproportionately large number of aggressive isolates, indicating fitness to survive and replicate on our best resistance sources.