Longleaf pine seed production is highly variable from year to year. This uncertainty complicates natural regeneration and the production of seedlings in forest tree nurseries for restoration plantings. Cone production is considered to be related to weather conditions, but the relationship is complex and no general models have been created. Forest Service scientists used the variability of cone production across years, at many different sites, to gain a better understanding of the complexity of factors influencing cone, and seed, production. Using a method of multiscale entropy, the scientists analyzed long-term cone crop data for longleaf pine at six sites across the southeastern U.S. The entropy of cone production for longleaf pine forests showed high linear correlation at all sites, increasing slowly through time, but remaining within 1.28 to 1.77. With similar dynamics at all sites, joint entropy reflected an emergent pattern for entropy across the Southern Region. Using information theory, the scientists’ analysis of entropy provides a useful approach for characterizing ecosystem dynamics by information flow in adaptive ecosystem management.