Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), is a severely devastating pest of Rutaceae plants, mainly citrus, across the globe, and causal agent of Huanglongbing (HLB) disease. To find out the genetic relationship and diversity among the populations of ACP and associated Candidatus Liberibacter asiaticus (CLas) from two countries (China and Pakistan), sequence data of three different genes, cytochrome oxidase subunit I (COI), Cu-transporting protein (ATOX1) and 16S rRNA, were used to characterize all populations. In the present study, MEGA-7 and statistical parsimony software (TCS-1.2) were used to depict the phylogenetic relationship among all populations under both genes, whereas diversity was calculated by DnaSP v5. All analyses were done for country wise and overall relationship among all populations. For ACP populations, both genes presented a significant strong intermingled relationship among all populations and put all population into a single haplotype (Dcit-2), which proved similarity between Chinese and Pakistani populations. Moreover, for CLas strains, 16S gene also presented strong relationship for all sampled populations. All three genes of ACP and CLas populations elucidated more than 95% resemblance to each other. On the other hand, a significant genetic variation was observed by three genes for overall populations, although, country wise variation was non-significant between all collected populations. ATOX1 gene presented higher diversity through Fu's Fs test (π = 0.01081, p < 0.003) whereas COI gene gave less diversity under Fu's Fs and Tajima's D test (π = 0.00512, p < 0.000 and 0.05, respectively). Similarly, nucleotide mismatch distribution also had shown enough genetic variation among all ACP populations, under both genes. Our sequence data for both genes proved the invasion of the Chinese ACP population (Dcit-2) into Pakistan, through all phylogenetic relationship, which proved a similar genetic makeup among all ACP populations from both countries. Therefore, these results can be helpful to utilize any novel designed control measure equally for both countries.