The subject of the study is discrete mathematical chemistry as a new field of knowledge in theoretical chemistry. Particular attention is paid to such aspects of research as: the characteristics of the stages of its development in connection with scientific and social problems, their connection with the formation of the subject and the features of methodology, the difference between discrete mathematical chemistry from mathematical chemistry, chemoinformatics and digital chemistry, the connection with these sciences is traced. The object of research is mathematical discrete chemistry in the context of its history. The methodology of the research includes the principle of the relationship between historical and logical, which made it possible to identify turning points in the history of discrete mathematical chemistry associated with its theorization, and a systematic approach, in which the hierarchy of mathematical models in modern mathematical chemical sciences is considered, revealing the peculiarity of the subject of discrete mathematical chemistry. It is concluded that discrete mathematical chemistry is an independent field of knowledge that arose as a result of the integration of methods of non-numerical mathematics and various fields of chemical knowledge. It has gradually emerged from various fields of chemical sciences, has its own specifics, which distinguishes it from mathematical chemistry, chemoinformatics and digital chemistry according to the following criteria: 1) the method of introducing discrete mathematics into chemistry without the participation of an intermediary in this process – physics, 2) a special style of mathematical thinking in chemistry, 3) the degree of idealization in mathematical modeling. Its mathematical apparatus is a mathematical modeling, which is used to formalize many chemical sciences. It is a research tool and the language of modern chemistry. The novelty of the research lies in the fact that the specificity of discrete mathematical chemistry is revealed, its identity and independence are established, and its methodological boundaries are determined in accordance with the hierarchy of mathematical chemical sciences. The research results contribute to the methodology of chemistry and the philosophy of science.