Key message The heritability of genetic resistance of radiata pine against Fusarium circinatum was not clear. We demonstrated that there are at least 3 QTLs that could be involved in this resistance/susceptibility. Abstract A genetic linkage map was developed for Pinus radiata, using Amplified Fragment Length Polymorphism (AFLP), Inter-Simple Sequence Repeat (ISSR), Selective Amplification of Microsatellite Polymorphic Loci (SAMPL), and Simple Sequence Repeat (SSR) molecular markers, based on a two-way pseudo-testcross strategy, using 86 individuals of a F1 full-sib family and 787 molecular markers for genotyping. Linkage analysis generated a map of medium to high density for each parent, with 1,060 and 1,258 cM for parents XO and XP, respectively. A total of 458 markers were mapped on 12 linkage groups (LG) in XO and XP, which equals the number of haploid chromosomes present in P. radiata. Analysis of quantitative trait loci (QTL) for resistance against pitch canker disease caused by Fusarium circinatum was made using Bayesian Information Criterion (BIC). In the XO parental map, two groups (LG-1 and LG-9) showed high probabilities for one or more QTLs. Only one group in the XP parental map showed probability for one or more QTLs. The results indicate that resistance to pitch canker is inherited from both parents. These results provide the basis for further studies focused on structure, evolution, and function of the P. radiata genome.