We reported the sequence and characteristics of the complete mitochondrial genome of an ecologically important stingless bee, Lepidotrigona flavibasis (Hymenoptera: Meliponini), that has suffered serious population declines in recent years. A phylogenetic analysis based on complete mitogenomes indicated that L. flavibasis was first clustered with another Lepidotrigona species (L. terminata) and then joined with the other two Melipona (Hymenoptera: Meliponini) stingless bees (M. scutellaris and M. bicolor), forming a single clade of stingless bees. The stingless bee clade has a closer relationship with bumblebees (Bombus) (Hymenoptera: Apidae) than with honeybees (Apis) (Hymenoptera: Apidae). Extremely high gene rearrangements involving tRNAs, rRNAs, D-loop regions, and protein-coding genes were observed in the Lepidotrigona mitogenomes, suggesting an overactive evolutionary status in Lepidotrigona species. These mitogenomic organization variations could provide a good system with which to understand the evolutionary history of Meliponini.

Lepidotrigona terminata (Smith, 1878) is a stingless bee that distributed in Eastern Asia. The complete mitogenome of L. terminata (GenBank accession number MN737481) is 15,431 bp in size, including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a noncoding D-loop region. The D-loop region is located between ND4L and tRNA^Met, different from the other two stingless bee mitogenomes previously reported. The base composition of the whole L. terminata mitogenome is 38.18% for A, 11.67% for G, 38.32% for T, and 11.83% for C, with a high AT bias of 76.50%. The present data could contribute to a detailed phylogeographic analysis of this valuable economic insect for further study in differentiating closely related species.