We sequenced complete mitochondrial genomes (mt genomes) of four Apis species, such as A. cerana, A. dorsata, A. laboriosa, and A. mellifera ligustica. The A. m. ligustica used in this study was originated from United States and selected for a high hygienic behavior during several years of breeding program. Considering current phylogenetic hypothesis of Apis the positive relationships between phylogeny and gene rearrangement was not supported. Phylogenetic reconstruction using available Apoidea species has shown the relationships ((Apidae + Colletidae) + Crabronidae). Within Apis, a strong support for three groups was obtained: A. florea and A. andreniformis as a basal group to the other A. cerana and A. mellifera group and A. dorsata and A. laboriosa group. The test to find out suitable single mt gene for the phylogeny at the genus level and below-genus level of Apis provided an identical topology from ND4L and ND6 in the ML analysis and ND3 and NF4L in the BI analysis to that from whole mt genome, with relatively strong support, indicating that these individual genes can potentially be utilized for within-species level phylogeny of Apis.