Exemplary embodiments support multi-threaded subgraph execution control within a graphical modeling or graphical programming environment. In an embodiment, a subgraph may be identified as a subset of blocks within a graphical model, or graphical program, or both. A subgraph initiator may explicitly execute the subgraph while maintaining data dependencies within the subgraph. Explicit signatures may be defined for the subgraph initiator and the subgraph either graphically or textually. Execution control may be branched wherein the data dependencies within the subgraph are maintained. Execution control may be joined together wherein the data dependencies within the subgraph are maintained. Exemplary embodiments may allow subgraphs to execute on different threads within a graphical modeling or programming environment.