Dispersal is a key influence on species' persistence, particularly in the context of habitat fragmentation and environmental change. Previously, residual population synchrony has been demonstrated to be an effective proxy for dispersal in mobile butterflies (Powney et al. 2012). Here, we highlight the utility and limitations of population synchrony as an indicator of functional connectivity and persistence, at a range of spatial scales, in a specialist, sedentary butterfly. While at the local scale, population synchrony is likely indicative of dispersal in the pearl-bordered fritillary, Boloria euphrosyne, over larger scales, habitat is likely to influence population dynamics. Although declines in local-scale synchrony conformed to typical movement in this species, synchrony showed no significant trend with distance when studied at larger (between-site) scales. By focusing on specific site comparisons, we draw the conclusion that heterogeneity in habitat successional stage drives asynchrony between sites at larger distances and is, therefore, likely to be a more important driver of population dynamics over large distances than dispersal. Within-site assessments of synchrony highlight differences in dispersal based on habitat type, with movement shown to be most inhibited between transect sections with contrasting habitat permeability. While synchrony has implications for metapopulation stability and extinction risk, no significant difference was found in average site synchrony between sites that had gone extinct during the study period and those remaining occupied. We demonstrate that population synchrony may be used to assess local-scale movement between sedentary populations, as well as to understand barriers to dispersal and guide conservation management.