The article presents an analysis of the main directions of transformations of the organs of the reproductive system during the evolution of vertebrates at various levels of the hierarchical organization of vertebrates - cellular, tissue, organ, organism, population. During the evolution of vertebrates, gonadal oligomerization occurred, a decrease in the number of hermaphrodite species, a decrease in the relative mass of gonads in the body, and a transition from isogamy to heterogamy (oogamy) was observed. In vertebrates, 4 types of structural and functional organization of male gonads have been formed: follicular type, follicular-cystic type, tubular-cystic type, tubular type. In representatives of different classes of vertebrates, the transformation of the ovaries proceeded in different directions. Large, grape-shaped ovaries have evolved in fish, amphibians, reptiles, birds, and cloacal mammals. These ovaries, just before the breeding season, can occupy almost the entire abdominal cavity. The ovaries of placental mammals are small in size, their shape is most often oval, the surface is smooth. One of the directions of the evolutionary transformation of the gonads was the compartmentalization of the structures of the male and female gonads, while there was a structural and topographic division into the actual gonads and the genital tract, which were formed on the basis of the structures of the primary kidney. Higher vertebrates have well-developed accessory sex glands. In the gonads, there was a clear topographical distinction between endocrine and germinal structures. Against the background of an increase in the number of species with internal fertilization, against the background of the formation of a complexly organized vagina and uterus in female mammals, the formation and complication of the copulatory organs of males occurred.