Functional-structural plant models (FSPMs) explore and integrate relationships between a plant's structure and processes that underlie its growth and development. In recent years, the range of topics being addressed by scientists interested in functional-structural plant modelling has expanded greatly. FSPM techniques are now being used to dynamically simulate growth and development occurring at the microscopic scale involving cell division in plant meristems to the macroscopic scales of whole plants and plant communities. The plant types studied also cover a broad spectrum from algae to trees. FSPM is highly interdisciplinary and involves scientists with backgrounds in plant physiology, plant anatomy, plant morphology, mathematics, computer science, cellular biology, ecology and agronomy. This special issue of Annals of Botany features selected papers that provide examples of comprehensive functional-structural models, models of key processes such as partitioning of resources, software for modelling plants and plant environments, data acquisition and processing techniques and applications of functional-structural plant models for agronomic purposes.