Early detection and management of dwarf mistletoe (Arceuthobium spp.) is currently limited by the inability to rapidly detect infection during the 2- to 5-year endophyte phase of the parasite. We describe a polymerase chain reaction (PCR) technique for detecting Arceuthobium douglasii Engelm. and Arceuthobium laricis Engelm. in tissues of its hosts, Pseudotsuga menziesii (Mirb.) Franco and Larix occidentalis Nutt. DNA was extracted from branches of 15 infected and 15 uninfected P. menziesii. The PCR product amplified by using the Arceuthobium specific primer in the rbcL gene from Arceuthobium template DNA was a fragment of 708 pairs of bases in length. This product was amplified from all branches that were visibly infected, but the fragment was not generated from any samples known to be uninfected. The PCR product from conifer DNA was a fragment of 385 pairs of bases in length and was not amplified from pure mistletoe DNA; this was amplified as an internal positive control. The primers developed for P. menziesii and A. douglasii also worked on L. occidentalis and A. laricis. This method detected mistletoe DNA in 7 of 29 P. menziesii branches and 3 of 21 L. occidentalis branches that did not have external symptoms of infection and are presumed to be the result of the endophyte phase. This method provides a useful tool for experimental applications and for managing the spread of dwarf mistletoe.