Stingless bees are a group of eusocial insects, they inhabit tropical and subtropical areas of the world and approximately 500 species are reported. In the pre-Hispanic era in Mesoamerica, vestiges of meliponiculture are reported; the relationship between the people of the civilizations of this time and the stingless bees had an important value in social, economic, and religious aspects. The objective of this study was to perform an ancestor-descendant bioinformatic analysis with molecular data (mtDNA) of the Meliponines. Nucleotide sequences of the COI-COII fragments of mtDNA were obtained from the Nucleotide sequence database at the National Center for Biotechnology Information (NCBI), using the search and Entrez functions. The fragments the sequences were aligned with cluster and then a phylogenetic analysis of the native bee species reported for Mexico in the NCBI was carried out. Based on the COI-COII mtDNA fragments, it was possible to build a phylogenetic tree, finding evolutionary relationships between the species, allowing to demonstrate that species of the Meliponini Tribe diverge from a more recent common ancestor to a less recent one.