Chemical studies of the plant family Annonaceae have intensified in the last several decades due to the discovery of annonaceous molecules with medicinal potential (e.g., benzylisoquinoline alkaloids and acetogenins). Approximately 500 alkaloids have been identified in 138 Annonaceae species in 43 genera. In addition, until 2004, 593 annonaceous acetogenins (ACGs) had been identified, from 51 species in 13 genera.This suggests that plants from this family allocate important resources to the biosynthesis of these compounds. Despite the diversity of these molecules, their biological roles, including their physiological and/or ecological functions, are not well understood. In this study, it was provided new data describing the variety and distribution of certain alkaloids and ACGs in annonaceous plants in distinct stages of development. The potential relationships among some of these compounds and the seasonally climatic changes occurring in the plant habitat are also discussed. These data will improve our understanding of the secondary metabolism of these pharmacologically important molecules and their expression patterns during development, which will help to determine the optimal growth conditions and harvest times for their production.