Purpose of research. The main idea is to build a mathematical testing model that integrates different aspects of an embedded reconfigurable computing system and its interactions. This model provides an efficient representation of test scenarios and allows to analyse the dynamics of the reconfigurable computing system during testing. The paper also discusses methods for generating test sequences based on the properties of a finite state machine.Methods. The authors propose to represent the autotest as a finite state Mile machine, where states serve to store information about the current state of an embedded reconfigurable computing system. The input signal is the interaction with the system and the output signal is the system's response to the input signal. This approach allows to formalize the testing process and simplify the analysis of possible problems.Results. This paper discusses the application of automata theory in the context of automated testing of embedded reconfigurable computing systems. Automata theory provides effective methods and tools for analysis and simulation of discrete dynamic systems, which makes it suitable for automated testing tasks.Conclusion. The results show that the use of automata theory can significantly improve the quality and efficiency of automated testing of embedded reconfigurable computing systems. This approach provides a deeper analysis of the system and allows to detect and prevent potential problems that may arise during its operation.