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Abstract Identifying patterns of pathogen infection in natural systems is crucial to understanding mechanisms of host–pathogen interactions. In this study, we explored how Junonia coenia densovirus (JcDV) infection varies over space and time in populations of the Melissa blue butterfly (Lycaeides melissa: Lycaenidae) using two different host plants. Collections ofL. melissaadults from multiple populations and years, along with host plant tissue and community samples of arthropods found on host plants, were screened to determine JcDV prevalence and load. Additionally, we sampled at multiple time points within a singleL. melissaflight season to investigate intra‐annual variation in infection patterns.We found population‐specific variation in viral prevalence ofL. melissaacross collection years, with historical samples potentially having higher viral prevalence than contemporary samples, although host plant diet was not informative for these patterns. Patterns of infection across multiple generations within a flight season showed that late‐season samples had a higher proportion of JcDV‐positive individuals, suggesting an accumulation of virus over the season. Sequence data from a segment of the JcDV capsid gene showed a lack of viral genetic diversity betweenL. melissacollected from different localities, and little to no viral particles were found in the surrounding environment.Our discovery of temporal variation in infection suggests that multiple sampling efforts must be made when describing pathogen prevalence in multivoltine hosts. Our findings represent an important first step towards further exploration of the ecological factors mediating disease prevalence and host‐specific variability of infection in wild insect populations.