Background: The whiteflies under the name Bemisia tabaci (Gennadius) (Aleyrodidae: Hemiptera) are species complex of at least 31 cryptic species some of which are globally invasive agricultural pests. Previously, the mitochondrial genome (mitogenome) of the indigenous New World B. tabaci species was sequenced and major differences of gene order from the postulated whitefly ancestral gene order were found. However, the sequence and gene order of mitogenomes in other B. tabaci species are unknown. In addition, the sequence divergences and gene expression profiles of mitogenomes in the B. tabaci species complex remain completely unexplored.Results: In this study, we obtained the complete mitogenome (15,632 bp) of the invasive Mediterranean (MED), which has been identified as the type species of the B. tabaci complex. It encodes 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs and 22 transfer RNAs (tRNA). Comparative analyses of the mitogenomes from MED and New World (previously published) species reveal that there are no gene arrangements. Based on the Illumina sequencing data, the gene expression profile of the MED mitogenome was analyzed. We found that a number of genes were polyadenylated and the partial stop codons in cox1, cox2 and nd5 are completed via polyadenylation that changed T to the TAA stop codon. In addition, combining the transcriptome with the sequence alignment data, the possible termination site of some PCGs were defined. Our analyses also revealed that atp6 and atp8, nd4 and nd4l, nd6 and cytb were found on the same cistronic transcripts, whereas the other mature mitochondrial transcripts were monocistronic. Furthermore, RT-PCR analyses of the mitochondrial PCGs expression in different developmental stages revealed that the expression level of individual mitochondrial genes varied in each developmental stage of nymph, pupa and adult. Interestingly, mRNA levels showed significant differences among genes located in the same transcription unit suggesting that mitochondrial mRNA abundance is heavily modulated by post-transcriptional regulation.Conclusions: This work provides novel insights into the mitogenome evolution of B. tabaci species and demonstrates that utilizing RNA-seq data to obtain the mitogenome and analyze mitochondrial gene expression characteristics is practical. © 2013 Wang et al.; licensee BioMed Central Ltd.