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This article presents a new control architecture designed for heterogeneous modular, multi-configurable, chained micro-robots. This architecture attempts to fill the gap that exists in heterogeneous modular robotics research, in which little work has been conducted compared to that in homogeneous modular robotics studies. The architecture proposes a three-layer structure with a behaviour-based, low-level embedded layer, a half-deliberative half-behaviour-based high layer for the central control, and a heterogeneous middle layer acting as a bridge between these two layers. This middle layer is very important because it allows the central control to treat all modules in the same manner, facilitating the control of the robot. A communication protocol and a module description language were also developed for the control architecture to facilitate communication and information flow between the heterogeneous modules and the central control. Owing to the heterogeneous behaviour of the architecture, the system can automatically reconfigure its actions to adapt to unpredicted events (such as actuator failure). Several behaviours (at low and high levels) are also presented here.