Aleppo pine is a thermophilic species that has become a popular tree species in plantings even beyond its natural habitat. In 1999 the pathogenic fungus Gremmeniella abietina was isolated for the first time in Aleppo pine plantations in Spain. The main objective of this study was to analyse the variation in susceptibility to G. abietina (European race, biotype A) infections among trees from five Aleppo pine provenances. Artificial inoculations were performed at two different times in January 2012. The susceptibility of the trees was evaluated by recording disease severity and the length of internal stem necrosis produced by the pathogen. In addition, the concentrations of two flavanone compounds were quantified as putative indicators of resistance. Provenances and G. abietina isolates both significantly affected levels of necrosis although the results were dependent on the time of inoculation. There was a relationship between provenance and resistance, with trees of higher elevation provenances being more susceptible to disease than trees of lower elevation provenances. The amount of naringenin flavanone from trees was significantly different between provenances, suggesting that it is a possible indicator value for resistance. Conversely, no differences were found in the concentration of eriodictyol in trees between provenances. The results show that the provenance-dependent variation in the susceptibility of Aleppo pine to G. abietina should be considered in selection of seed sources for restoration.