The interaction between hosts and pathogens and the severity of epidemics, depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity. We assessed and compared the diversity of a fungal pathogen, Pyrenophora teres fsp. teres, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites and pathogenicity to assess the importance of weeds in the evolution of this pathogen. The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and has a higher effective population size. Thus, pathogen census population size is a better predictor for neutral genetic diversity than host diversity. However, the pathogen populations on the two hosts are distinct based on clustering of their microsatellite alleles and most importantly, do not show cross host pathogenicity. Thus, although weeds enhance the evolution of aggressiveness in some other pathosystems, here barley grass poses no threat to increased aggressiveness evolution of Pyrenophora teres fsp. teres on barley.