In this paper, we present PlantGL, an open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants. This C++ geometric library is embedded in the Python language which makes it a powerful user-interactive platform for plant modeling in various biological application domains. PlantGL makes it possible to build and manipulate geometric models of plants or plant parts, ranging from tissues and organs to plant populations. Based on a scene graph augmented with primitives dedicated to plant representation, several methods are provided to create plant architectures from either field measurements or procedural algorithms. Because they are particularly useful in plant design and analysis, special attention has been paid to the definition and use of branching system envelopes. Several examples from different modelling applications illustrate how PlantGL can be used to construct, analyse or manipulate geometric models at different scales ranging from tissues to plant communities.