In the process of identifying around 15,000 missing persons by the armed violence in Peru (1980-2000), the major problem is the high probability of random matches in especial of Andean Ayacucho population which represents the largest number of missing persons. To that end, in a first analysis, we analyzed the relationships and genetic structure in 880 individuals from 20 regions of Peru (including Ayacucho) with IDENTIFILER Kit and in a second analysis; we studied 203 individuals of Ayacucho using the ARGUS-X and ESSPLEX_SE Kit with the aim to confirm the intrapopulation structure found in the first analysis. In the first analysis using the delta-mu parameter, clearly shows three genetic groups at the national level (North, Central and South) with a low variability among groups but significative with AMOVA (0.47%** (P< 0.01)). In the tree, Ayacucho population is located in the south group and interestingly showed a significative FIS (0.10** (P< 0.01)). The second analysis confirm this FIS but lowest (FIS = 0.06) and this FIS could be explained by the evidence of a recent bottleneck found under the IAM, SMM and TPM models (P< 0.01). On the other hand, the X-STR show low probability of random match than in Autosomic STR which may be related to content of admixture among native and foreign populations (30% foreign content in Peruvian population). The results in this study are consistent with the demographic history (processes of migration, immigration, inbreeding), which contribute to the increase of IBDs and may be related to the random match DNA identification. © 2011 Elsevier Ireland Ltd.