In this study, partial sequences of the mitochondrial cytochrome oxidase subunit Ⅰ (mtDNA-COI) gene and the ribosomal internal transcribed spacer 1 (rDNA-ITS1) gene, isolated from five artificial populations of Liriomyza sativae (Diptera:Agromyzidae), were sequenced and compared, to analyze their genetic variation. Analysis of the mtDNA-CO1 gene showed that a low genetic variation was detected among the five populations and only five variable sites were found in the nucleotide sequences. Most of the observed variations that occurred within the populations were because of nucleotide transitions, whereas, the interpopulation variation was because of the differences in haplotype frequencies occurring among the host populations. Analysis of the rDNA-ITS1 gene revealed a small diversity in the five host populations. The trend of genetic differentiation in the host populations was consistent with the preference of L. sativae to the plant hosts.