Whole genome amplification protocols are revolutionizing the fields of molecular and conservation biology as they open the possibility of obtaining a large number of copies of a complete genome from minute amounts of sample. Multiple displacement amplification (MDA) is a whole genome amplification technique based on the properties of the phi29 DNA polymerase, which leads to a uniform representation of the genome with very low error rates. In this study we performed MDA on 28 macaque DNA samples extracted from blood or non-invasively collected semen from which we obtained mitochondrial control region sequences both before and after MDA. The length of the readable sequences was longer for the original samples than for the MDA products, but the number of unresolved positions was comparable both before and after MDA. We conclude that the MDA technique is useful for increasing the amount of DNA for sequencing mitochondrial regions in the case of non-invasively collected semen samples.