Whether a perceived increase in the abundance of jellyfishes is related to changing marine environments has been considered primarily using large-scale analyses of multi-species assemblages. Yet jellyfish blooms—rapid increases in the biomass of pelagic coelenterate species—are single-species demographic events. Using published and new genetic analyses and population surveys, we investigate whether there may be a critical knowledge gap between the scales of recent analyses and the scales of natural phenomena. We find that scyphomedusae may show population genetic structure over scales of tens to hundreds of kilometers, that environments vary regionally and locally, and that populations of medusae can display uncorrelated dynamics on these scales. These findings suggest genetic differences between populations and/or environmental differences between sites are important determinants of population dynamics in these jellyfishes. Moreover, the local abundance of medusae may be most strongly correlated with preceding rather than current local environmental conditions, indicating there is a cumulative time-course to the formation of ‘blooms’. Broad-scale macro-ecological analyses will need to build from coordinated, long-term, fine-grained studies to synthesize, rather than mask, population-level phenomena in larger-scale analyses.