Qualitative analysis of three-dimensional deterministic mathematical models of population dynamics of two types is performed: the model which takes into account the competition and diffusion of species and the model of interaction of populations which takes into account mutual interaction between the species. The combination of known methods of synthesis and analysis, and developed method of construction of stochastic self-consistent models is used in the research of these methods. Existence conditions of equilibrium states are obtained and the analysis of stability is performed. The corresponding nondeterministic mathematical models are constructed by means of transition from ordinary differential equations to differential inclusions, fuzzy and stochastic differential equations. Using the principle of reduction, which allows us to study stability properties of one type of equations, using stability properties of other types of equations, as a basis, sufficient conditions of stability are obtained. The synthesis of the corresponding stochastic models on the basis of application of the method of construction of stochastic self-consistent models is performed. The structure of these stochastic models is described, Fokker-Planck equations are given, the rules of transition to the stochastic differential equation in the form of Langevin are formulated, and computer simulation is carried out. The obtained results are aimed at the further development of methods of construction and the analysis of nondeterministic mathematical models of natural sciences with carrying out computer experiments.