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Habitat loss and forest fragmentation are often linked to increased pathogen transmission, but the extent to which habitat isolation and landscape connectivity affect disease dynamics through movement of disease vectors and reservoir hosts has not been well examined. Tick-borne diseases are the most prevalent vector-borne diseases in the United States and on the West Coast,Ixodes pacificusis one of the most epidemiologically important vectors. We investigated the impacts of habitat fragmentation on pathogens transmitted byI. pacificusand sought to disentangle the effects of wildlife communities and landscape metrics predictive of pathogen diversity, prevalence and distribution. We collected pathogen data for four co-occurring bacteria transmitted byI. pacificusand measured wildlife parameters. We also used spatial data and cost-distance analysis integrating expert opinions to assess landscape metrics of habitat fragmentation. We found that landscape metrics were significant predictors of tick density and pathogen prevalence. However, wildlife variables were essential when predicting the prevalence and distribution of pathogens reliant on wildlife reservoir hosts for maintenance. We found that landscape structure was an informative predictor of tick-borne pathogen richness in an urban matrix. Our work highlights the implications of large-scale land management on human disease risk.