A pair of primers specific for Neonectria galligena were designed from comparisons of the internal transcribed spacer (ITS) regions 1 and 2 of 32 isolates of diverse origins with sequences from 7 other nectriaceous species: ‘Nectria’ ditissima, N. coccinea, N. coccinea var. faginata, N. punicea, N. fuckeliana, N. cinnabarina, and N. radicicola. Comparisons were also made with sequences from several commonly encountered fungal endophyte species of apple wood, in particular Fusarium lateritium. Under stringent PCR conditions, primers Ch1 and Ch2 amplify a 412 bp fragment from N. galligena DNA nectriaceous but not from other nectriaceous species, fungal apple endophyte species, rosaceous, or beech host tissues. The identity of PCR products from total DNA extracts from woody tissues was confirmed by Southern hybridization. A 500 bp heterologous internal standard incorporating identical primer recognition sites was generated for use as an internal positive control for individual PCR assays to identify false negatives due to the presence of high levels of co-precipitated PCR inhibitory compounds. Further adaptation of this approach allowed for semi-quantitative competitive PCR enabling the determination of target fungal levels in infected lignified tissues.