The Asian citrus psyllid, Diaphorina citri, is a major threat to citrus production worldwide, as it transmits 'Candidatus Liberibacter asiaticus', the pathogen associated with the devastating Asian form of huanglongbing. The psyllid has spread widely from its native South Asia during the past 300 years, most recently to Africa. We report the first population genomic analyses of D. citri in Kenya and La Réunion based on next-generation sequencing of their mitochondrial genomes. We analyzed mitochondrial sequences of 264 D. citri individuals to establish genetic relationships among accessions from D. citri populations from Asia, North America and Africa. Haplotype network analysis indicated that the psyllids from Kenya were genetically close to an accession from Cambodia, and distinctly different to those from La Réunion. These findings revealed populations in southern Indochina would be the likely source of the D. citri introduction into East Africa through human-mediated transfer of psyllid-infested plants.