According to the data on the Y-chromosome polymorphism, an assessment of the influence of two factors (tribal (clan) and administrative (kozhuuns) subdivision) on the structure of the gene pool of Tuvans is provided. The ten most common Tuvan clans (Ak, Baraan, Irgit, Kol, Kyrgyz, Mongush, Oorzhak, Oyun, Khertek, Choodu) are included in this analysis. They cover two-thirds of the total sample (N = 545) of Tuvans from six kozhuuns (Barun-Khemchiksky, Tandinsky, Tere-Kholsky, Todzhinsky, Chaa-Kholsky, Erzinsky). Genetic portraits of clans created on the basis of 52 SNP markers of the Y chromosome reveal the founder effect for all clans, except the two largest-Kyrgyz and Mongush. Making up one-third of the sample, these two clans are conglomerates. Analysis of molecular variance (AMOVA) indicates an equal degree of genetic separation of clans (5.2%) and kozhuuns (6.8%). But the Mantel test detects a high correlation (r = 0.50) between the genetic and clan structure against the low correlation (r = 0.25) between the genetic and geographical distances. The reason for the difference between the AMOVA and Mantel test lies in the fact that the four most numerous kozhuuns are "monoclan," in which one clan prevails, and only two kozhuuns (Todzhinsky and Tere-Kholsky) include representatives of three different clans. The selection of the western and eastern clusters on the graph of multidimensional scaling fits in well with the anthropological data (Sayansky and Katangsky anthropological types), but does not confirm any of the ethnographic versions of the Tuvan ethnogenesis ("Samoyedic," "Mongolian," "Turkic"). The sum of results indicates that the tribal structure most fully reflects the architectonics of the Tuvan gene pool, and for this reason, it must be taken into account in population genetic research.