Dothistroma septosporum and D. pini cause the serious pine needle disease, Dothistroma needle blight (DNB). Of these, D. septosporum has a global distribution, while D. pini is known only from the USA, Russia, Ukraine and France. During a study of D. septosporum isolates from Pinus nigra in Hungary, microsatellite markers revealed the presence of a second Dothistroma species. The aim of this study was to identify the DNB pathogens occurring in Hungary using four different molecular techniques. These included sequencing of the rDNA ITS region, a species-specific ITS-RFLP, mating type primers and a diagnostic microsatellite marker, Doth_A. Results showed that both D. septosporum and D. pini occur in Hungary and that both DNB pathogens were present on the same trees and in some cases, the same needles. Mating types MAT1 and MAT2 of D. septosporum were shown to be present in Hungary, but only the MAT2 of D. pini was found. In addition, examination of needles with DNB symptoms from Russia revealed the presence of D. pini on Pinus pallasiana and P. nigra as well as on a new host, Pinus mugo. The molecular markers applied in this study were sufficiently robust to identify and differentiate between the two DNB pathogens, both in culture and directly from needles. They will consequently be useful to document the geographical range and to monitor the spread of D. septosporum and D. pini in future studies.