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The environment has a strong influence on the abundance and distribution of plant pathogenic organisms and plays a major role in plant disease. Climatological factors may also alter the dynamics of the interactions between plant pathogens and their hosts. Nothophaeocryptopus (=Phaeocryptopus) gaeumannii, the causal agent of Swiss needle cast (SNC) of Douglas-fir, is endemic to western North America where it exists as two sympatric, reproductively isolated lineages. The abundance of this fungus and the severity of SNC are strongly influenced by climate. We used statistical and population genetic analyses to examine relationships between environment, pathogen population structure, and SNC severity. Although N. gaeumannii Lineage 2 in western Oregon and Washington was most abundant where SNC symptoms were most severe, we did not detect a significant relationship between Lineage 2 and disease severity. Warmer winter temperatures were inversely correlated with foliage retention (AFR) and positively correlated with the relative abundance of Lineage 2 (PL2). However when distance inland, which was strongly correlated with both AFR and PL2, was included in the model, there was no significant relationship between Lineage 2 and AFR. Spring/early summer dew point temperatures also were positively associated with total N. gaeumannii abundance (colonization index (CI)) and inversely correlated with AFR. Warmer summer mean temperatures were associated with lower CI and higher AFR. Our results suggest that the two lineages have overlapping environmental optima, but slightly different tolerance ranges. Lineage 2 was absent from more inland sites where winters are colder and summers are warm and dry, while Lineage 1 occurred at most sites across an environmental gradient suggesting broader environmental tolerance. These relationships suggest that climate influences the abundance and distribution of this ecologically important plant pathogen and may have played a role in the evolutionary divergence of these two cryptic fungal lineages.