The aim of this work is the reconstruction, through genetics, of the history of Mesoamerican populations. For that, two strategies have been used, on the one hand five indigenous populations have been characterized using 15 autosomal markers (STRs) and different statistical methods (FST amova and mds) have been applied. On the other hand three new populations have been added including STRs more being those 3 STRs, the tnicrosatellites number shared by the eight populations. Coalescence times have been also calculated testing the possible existence of genetic barriers. The native American groups have a common origin and their rich genetic and cultural diversity can be explained by a model of rapid population expansion and local adaptations to different micro-habitats. This process, similar to that oftribalization, potentiated the existence of a genetic substructure justified by geographical and historical-linguistic parameters related in turn, to survival strategies and its demographic consequences. The divergence times between indigenous groups coincide with the archaeological information and determine that the fragmentation between Mesoamerican and Aridoamérica occurred during Lytic Period. It also confirms that Otomies could be one of the most ancient peoples of Mesoamérica and that Maya were fractionated from highland groups about 3 000 years ago. The most active periods, referring to population fragmentation, match with the Preclassic and the Postclassic, being the Colonial and the Classic more stable. Finally the importance of the acculturation phenomenon and gene flow was determined in order to understand the importance that have in the interpretation of genetic data. [ABSTRACT FROM AUTHOR]