The concept and content of control are important components of the theory and methodic of physical culture and sports. The consistency in processes and objective corrections of certain actions (processes) are provided by using of control. Actualization of scientific issues of control in the context of reforming the structure and content of higher education is gaining new importance. This is due to the higher dynamism and student-centered character of modern education. An urgent scientific and applied problem of modern physical education in higher education institutions is the substantiation of a systematic approach to training students swimming that will take into account existing experience and modern requirements. The purpose of the study was to substantiate the control subsystem in the training students swimming in higher education institutions during physical education. Material and methods: theoretical analysis and generalization, study of documentary materials, sociological methods of survey (questionnaire), system analysis, historical and logical research methods. Results and discussion. The control subsystem for the most aspects is management by a higher order system due to the close relationship with the control source, placement trends and the objectivity benefits. This subsystem is the basis for the differentiation of parts and at the same time for integration with the establishment of the organic unity of the whole system components. The key requirement for conducting control in the physical education condition in higher education institution is compliance with the specifics of the sport means as a variable component of the education content. Specific features of swimming have an important value for choosing complex of indicators. In the theoretical substantiation of control, there was observed requirements that are specified in the scientific and methodical literature. Among them are: availability of interval scale, reliability, validity, discriminativeness, availability of normative data, adaptability of the test, ease of execution and simplicity, limitation of test tasks, operationalization and verification of these tests / control exercises). It also takes into account a number of additional requirements for simplicity and low resource costs, regardless of the level of tests complexity, clarity and accessibility for teacher and student, conciseness and accuracy of execution instructions, the absence of external stimuli. Conclusion. Control is a fundamental element of conscious systemic human activity. The result of solving the generalized purpose of the system should be understood, accepted and acceptable to all participants of this process. Substantiation of the control subsystem of the training swimming system involves the formulation of a new category of individually-oriented content of control of students of higher education institutions and its variants. These variants must be built taking into account objective factors (the presence of different groups of students on the level of swimming preparedness, individual-motivational orientation of activity and trajectory of goal setting in the system of training swimming during physical education)