A sample of 15 blackfly (Diptera: Simuliidae) species collected in Quebec as larval specimens is used to evaluate COI, COII and 18S rDNA for their abilities to resolve distinct levels of evolutionary depth. Following characterization of the mutation pattern, the COI and COII computer simulations show that too frequent base interchanges at the degenerate third codon position quickly lead to early mutation saturation and to a loss of phylogenetic resolution. However, both mtDNA markers appear well suited for distinguishing closely related species. Molecular evidence also sheds doubts on the value of morphology alone for classifying Prosimuliini larvae, up to the point of calling for a taxonomic reappraisal of the whole tribe. At the opposite end of the phylogenetic spectrum, 18S elucidates remote divergence events while losing resolving power at low levels due to sequence conservatism as embodied by a limited number of informative sites being concentrated within two hot spot regions. In an attempt to fill the gap between ancient and recent divergence events, a composite tree was built from 18S, ITS2 and the COI/COII codons undergoing amino acid changes. Results show that a well weighed combination of markers evolving on different time scales can cover multiple taxonomic levels.