Craneflies (Tipuloidea or Tipulidae sensu lato) are one of the most diverse groups of true flies (Insecta, Diptera). The Tipuloidea and perhaps the Trichoceridae formed the infraorder Tipulomorpha, which is traditionally considered the most basal group of Diptera. Relationships among Tipulomorpha and the phylogenetic position of this infraorder within the whole Diptera remain to be settled. A mitochondrial genome (mitogenome) phylogeny of Diptera was produced to test the relationships within Tipulomorpha and its phylogenetic position. A complete mitogenome of Nephrotoma scalaris parvinotata (Tipuloidea, Tipulidae) was firstly sequenced with a nextgeneration sequencing approach. Compared with the published mitogenomes of Tipuloidea, the new mitoge nome had a larger genome size (17,862 nt), due to a longer non-coding control region. The gene order was identical to Drosophila yakuba. Phylogenetic reconstructions using different inference methods recovered Tipu lomorpha as monophyletic. And the Tipulomorpha was retrieved in a relatively basal position in Diptera. Within Tipulomorpha, the Tipuloidea and the Trichoceridae were strongly supported as reciprocally monophyletic. Relationships within Tipuloidea were resolved as (Pedicidae + (Limoniidae + (Cylindrotomidae + Tipulidae))). Well supported relationships include: Pedicidae was the sister group of (Limoniidae + (Tipulidae + Cylin drotomidae)); Limoniidae was paraphyletic with respect to (Tipulidae + Cylindrotomidae); Cylindrotomidae was the sister group of Tipulidae. The newly sequenced N. scalaris parvinotata clustered with other two Nephrotoma species at a derived position in Tipuloidea.