Polyphagotarsonemus latus Banks is considered a polyphagous pest of diverse agricultural and ornamental crops of global economic significance. Its distribution, host range, variety of symptoms, morphological differences, chaetotaxy and several ontogeny reports have advanced the idea of P. latus as a species complex. Correct pest identification leads to suitable control treatment. Therefore, the objective of this study was the identification of mites collected in two different geographic regions in Mexico (Chiapas and Guanajuato) that had been tentatively designated as Polyphagotarsonemus sp. Biometric differences on the morphology of adults as well the genetic variability were determined by taxonomical and molecular (mitochondrial COI gene) characterization techniques. The identity of the mites from both populations was confirmed as P. latus based on taxonomic characters. Biometric parameter variations were found between both populations (70.58% and 53.84% for females and males, respectively). The average sequenced fragment size was 447 bp (both populations). A homology search against six P. latus sequences available in the GenBank database revealed that sequence KM580507.1 (from India) shows 83.0-86.41% and 99.26-99.52% similarity with the sequences from Guanajuato and Chiapas, respectively. Molecular data indicated a significant divergence between the populations. The genetic distance demonstrates the population from Chiapas has a higher genetic correspondence (0.010) to the sequence from India (KM580507.1) whereas the population from Guanajuato is more distant (0.191). The genetic distance between the populations of this study and other GenBank sequences is even larger. We consider our results strengthen the hypothesis of P. latus consisting of a species-complex. However, it is essential to extend the study to other regions including its country of origin (Sri Lanka), and to include ultrastructural features.