The effects of the demographic history of mankind have led to the fact that the indigenous peoples of Dagestan and Siberia are inferior in terms of genetic diversity to the populations of Europe, which affects the level of identification informativeness of standard forensic autosomal markers in these populations. In our study, we evaluated the effectiveness of two standard sets of autosomal STRs (13 CODIS, 20 CODIS, Combined DNA Index System) for the genetic examination of parent–child relationship in four highly inbred populations of the Russian Federation and the Russian population, using two types of reference frequencies. The results of the study confirmed the assumption that the level of identification informativity of standard autosomal markers in highly inbred populations of Siberia and Dagestan is lower than in the Russian population. The total information content of markers of the new CODIS standard exceeds the threshold values required in the order of the Ministry of Health and Social Development of the Russian Federation (no. 346n). At the same time, the probability of a false positive result increases with an increase in the inbreeding coefficient in the population.