In order to reveal the phylogenetic relationships of Holometabola, the fragments of 18S rDNA gene of 21 species in 21 families of 11 orders from Holometabola and 3 species in 3 orders from Paraneoptera as outgroups are used in the current analysis. After the alignment of the sequences, the likelihood ratio test is carried out to find the best model of nucleotide substitution fitting the data obtained from the alignment. The molecular phylogenetic trees are reconstructed with ML and Bayesian methods. The hierarchical likelihood ratio test is used to analyze the dataset. The result suggests a division into three large clades comprising Diptera+Strepsiptera, Coleoptera+(Megaloptera+(Raphidioptera+Neuroptera)) and Hymenoptera+(Siphonaptera+Mecoptera)+(Lepidoptera+Trichoptera) in the cladogram of Endopterygota. Mecopterida is not a monophyly.