The Pacific oyster culture in Mexico began 45 years ago, first with spat imported from the USA and now with spat produced in several local hatcheries. Oyster farmers do not know the parameters that define the quality of the spat they buy, among them the level of genetic variability available in the lots offered. In order to evaluate and compare the genetic variability in spat produced by four Mexican hatcheries, an attempt was made to amplify and sequence the non-coding region and the ND5 gene of the oyster mitochondrial DNA with oligos reported in the scientific literature. The amplification of the non-coding region was not possible due to the bad design of the oligos. Despite the integrity of the extracted oyster DNA, the ND5 gene was not able to be amplified possibly due to the modification of the oligo recognition site in the gene. The generational separation of the oyster cultivated in Mexico from its original source population makes it necessary to obtain new mitochondrial sequences in order to design new oligos suitable for the populations established in Mexico.