The spotted wing drosophila, Drosophila suzukii Matsumura, affects berry (Fragaria L., Rubus L., and Vaccinium L.) production and is under official mitigation and surveillance in Mexico. To obtain biological information about the pest, a sample of six adult males and six adult females from CNRF breeding (Colima, Mexico) was studied. PCR was used to amplify regions of the X chromosome. Six markers (FBgn0001083, FBgn0017651, FBgn0026206, FBgn0029789, FBgn0029997, and FBgn0030437) were identified and their sequences were processed with different bioinformatic systems to build a network of haplotypes associated with their geographical distribution. The sequenced markers had similarities with those from populations in the United States (Florida, Georgia, Hawaii, and Massachusetts) and Japan.