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Here we report the complete mitochondrial sequences of 70 individual field collected mosquito specimens from throughout Sub-Saharan Africa. We generated this dataset to identify species specific markers for the following  Anopheles  species and chromosomal forms:  An. arabiensis ,  An. coluzzii  (The  Forest  and  Mopti  chromosomal forms) and  An. gambiae  (The  Bamako  and  Savannah  chromosomal forms).  The raw Illumina sequencing reads were mapped to the NC_002084 reference mitogenome sequence. A total of 783 single nucleotide polymorphisms (SNPs) were detected on the mitochondrial genome, of which 460 are singletons (58.7%). None of these SNPs are suitable as molecular markers to distinguish among  An. arabiensis ,  An. coluzzii  and  An. gambiae  or any of the chromosomal forms. The lack of species or chromosomal form specific markers is also reflected in the constructed phylogenetic tree, which shows no clear division among the operational taxonomic units considered here.

Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division