Abstract: The mitochondrial genome of insects has been proven to be a useful genetic marker for molecular and evolutionary studies. Tephritidae of Diptera is the most agriculturally important worldwide serious pests. The objective of this study is to infer phylogenetic relationships among 8 sequenced mitochondrial genomes within Tephritidae. According to conserved (C)/variable (V) sites ratio test, all 13 mtDNA Protein Coding Genes (PCGs) were combined into a single data set for use in determining phylogeny. The same gene regions of Pteronarcys princeps, Lucilia sericata and Drosophila yakuba were used as outgroup. When MP and ML analysis were applied to the combined data set, two fairly similar trees were shown. Accorded with all previous morphological and molecular evidence, the monophyly of family Tephritidae was strongly recovered in our result. The data set led to a likelihood tree in which B. dorsalis and B. papayae was provided relative closely relationship meanwhile B. carambolae formed a clade basal to them.