Abstract: The RNA secondary structure contains more information than its primary structure, and can indicate the phylogenetic relationship more really. Therefore, the complete sequences of mitochondrial L-rRNA genes of Bactrocera cucurbitae and B. correcta were sequenced in this study, and the structural model of L-rRNA genes in Diptera was constructed. The characteristics of L-rRNA secondary structure was analyzed, and preliminary phylogenetic features were inferred based on stem-loop parameters and structural sequences of H45-H47, and structural sequences of L-rRNA genes among 13 families in Diptera. The results showed that the dipterans share the conserved secondary structure of L-rRNA gene; the nucleotide composition and distribution vary within different structure regions of L-rRNA gene; the highest content of completely conserved nucleotides was found in region Ⅳ and Ⅴ; the region Ⅳ and Ⅴ also contains the highest GC content; the AT-skew is negative in region Ⅵ of L-rRNA gene of the majority of dipteran families; the unique bases within individual family and individually conserved nucleotides between families present higher content of G or C. The family Cecidomyiidae exhibits much farther distance with other dipteran families, while Calliphoridae, Tachinidae and Syrphidae share much closer phylogenetic relationship; Tabanidae and Nemestrinidae belong to a small branch; Ceratopogonidae and Culicidae share a large phylogenetic branch. The satisfied phylogenetic result would not be obtained easily using single phylogenetic parameter, and it is thus necessary to infer accurate phylogenesis through combined parameters of different features.

Key words: Diptera, Bactrocera correcta, Bactrocera cucurbitae, L-rRNA gene, sequencing, secondary structure, structural characteristics, phylogenesis