Abstract <p>The marriage structure of the Moscow population was analyzed as part of the study of genetic-demographic processes in modern megalopolises. The source for the study was the data of a questionnaire survey of virtually healthy residents of Moscow in two age groups: the “older” group (average year of birth: men—1949, women—1948) and the “younger” group (average year of birth: men—1985, women—1988). The level of intraethnic assortative mating was calculated (in Russians, the index of positive assortative mating is 75% in the “older” group and 88% in the “younger” group). The results of analysis of calculation of marital distances revealed that, in the “younger” group of the Moscow population, the average marital distance is 2.5 times greater than in the “older” group. In the “older” group of Muscovites, the proportion of interethnic marriages is about 10% and in the “younger” group, it is slightly higher—about 12%. In the “older” group of the Moscow population, the average level of exogamy is 0.97 ± 0.09 (σ = 1.31). In the “younger” group, the average level of exogamy is significantly higher—1.95 ± 0.11 (σ = 1.19). In the “older” group, the flow of “foreign” genes is greater by the father’s line than by the mother’s line (2Y flow is 9% and 2mt flow is 6%). In the “younger” group, on the contrary, there are slightly more “foreign” genes in the mother’s line (2Y flow is 8% and 2mt flow is 12%). The analysis of the marriage structure of the population from two different groups of Moscow showed an increase in the values of marital distances by generations (calculated for the most numerous nationality, i.e., both spouses are Russians) and, also, an increase in the average level of exogamy (in accordance with the previously defined increase in intensity and distance of migration to the megalopolis); gender features of gene flows into the gene pool of megalopolis correspond to the structure of migration and differences in parameters of the marriage structure between generations in the population of Moscow.</p>