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Abstract BackgroundAs habitat fragmentation increases, ecological processes, including patterns of vector-borne pathogen prevalence, will likely be disrupted, but ongoing investigations are necessary to examine this relationship. Here, we report the differences in the prevalence of Lyme disease (Borrelia burgdorferisensu lato, s.l.) and haemoproteosis (Haemoproteusspp.) pathogens in avian populations of a fragmented habitat.B. burgdorferis.l. is a generalist pathogen that is transmitted byIxodes pacificusvectors in California, andHaemoproteusis an avian parasite transmitted byCulicoidesvectors. MethodsTo determine whether biotic (avian and mammalian abundance) or abiotic characteristics (patch size and water availability) correlated with infection prevalence change, we screened 176 birds sampled across seven sites in oak woodland habitat in northern California. ResultsWhile biotic factors correlated with an increase in both pathogens, infection prevalence ofHaemoproteusspp. was only associated with individual-level traits, specifically foraging substrate and diet, andB. burgdorferis.l. was associated with community-level characteristics, both total mammal and, specifically, rodent abundance. Proximity to water was the only abiotic factor found to be significant for both pathogens and reinforces the importance of water availability for transmission cycles. Larger patch sizes did not significantly affect infection prevalence ofHaemoproteus,but did increase the prevalence ofB. burgdorferi. ConclusionsThese results highlight that while environmental factors (specifically habitat fragmentation) have a limited role in vector-borne pathogen prevalence, the indirect impact to biotic factors (community composition) can have consequences for bothHaemoproteusandB. burgdorferiprevalence in birds. Given the pervasiveness of habitat fragmentation, our results are of broad significance. Graphical abstract