Mitochondrial DNA sequences from COII and flanking regions were retrieved from 42 species of Chironomidae belonging to the genera Cladotanytarsus, Corynocera, Diplocladius, Eukiefferiella, Lauterborniella, Micropsectra, Orthocladius, Pagastiella, Paratanytarsus, Psectroladius, Prodiamesa, Rheotanytarsus, Stempellinella, Sergentia, Stictochironomus and Tanytarsus. Some Tanytarsini have unusually long intergenic regions between COII and the flanking tRNAs. Length variation of the COII gene is associated with hypervariable regions including internal indels. We discuss the possibility that flanking tRNAs and intergenic repeat patterns may make COII susceptible to small scale rearrangements. These mutational patterns are not assumed to disturb the functionality because the polypeptides can be folded to the 3D structure described by the Swiss Model, and putative copper binding active sites in Anopheles COII are conserved in the chironomids. Phylogeny was inferred on COII data using maximum parsimony and Bayesian analyses. A general time reversible model accounting for the proportion of invariable sites and with gamma correction for nucleotide substitution rate heterogeneity (GTR+Γ+Ι) was found as the best model for evolutionary change. Implementation of the model in Bayesian analyses recovered a phylogenetic consensus tree that corresponds well with the hypothesis of Tanytarsini relationships derived from morphological studies. High probabilities were estimated for monophyly of the genera examined, except that Corynocera ambigua becomes the sister taxon of Tanytarsus gracilentus. The tree is also in agreement with the taxonomic division of subtribes Tanytarsina and Zavreliina. However, the data and model only weakly support many of the suggested relationships between the genera of Tanytarsini.