The Asian citrus psyllid, Diaphorina citri Kuwayama, is native to Asia but has recently invaded North America. Asian citrus psyllid is a significant pest of citrus crops by its direct feeding but, more importantly, as the vector of the bacterium ‘Candidatus Liberibacter asiaticus’, which causes Huanglongbing disease. Asian citrus psyllid was first found in México in 2001 and 2002 and, since then, has spread quickly across the country, suggesting rapid adaptation to new environments. Yet, we lack information on the genetic variation and structure that could facilitate or inhibit adaptation. Using six microsatellite markers, we analyzed genetic variation and structure among six localities in México: three in western states near the Pacific coast and two in the Yucatán Peninsula near the Gulf of México. We found low genetic diversity (no more than three alleles per locus) and intermediate differentiation between all populations. Asian citrus psyllid populations clustered into two genetic groups, but, surprisingly, these clusters were present in western populations. The first group included El Arenal, and the second group included Autlán de Navarro, Colima, and Tecomán. Interestingly, both of the Yucatán populations shared variation from the two clusters, suggesting admixture. We infer that reproductive isolation, barriers to gene flow, local selection, and the possibility of multiple invasions have influenced the current genetic structure of Asian citrus psyllid in México.