Classical studies on the insect vectors of parasitic diseases have relied on morphological, biochemical and cytological characters to classify vector species. These are often inadequate for a detailed dissection of the dynamics of the parasite-vector relationship. Molecular techniques have the potential to provide move reliable data on various aspects of vector biology, including population genetics, molecular phylogenetics, and molecular differentiation and classification of closely related species. However, most molecular techniques are expensive, cumbersome or difficult to apply to the analysis of a large number of samples. Here, Jianming Tang and Tom Unnasch discuss the practical advantages of heteroduplex analysis for the study of medically important vectors, using the black flies that serve as vectors for the filarial parasite Onchocerca volvulus as an example. This technique is simple, rapid, inexpensive and capable of detecting minor differences among DNA sequences.