Identifying genes conferring tolerance to fungal diseases is highly desired for resistance breeding in rubber. Resistance traits are mainly quantitative in nature and are determined by many genes and gene complexes, which are described as quantitative trait loci (QTL). Interspecific cross between H. brasiliensis (clone RRII 105) and H. benthamiana (clone F4542) with varying levels of disease resistance was made and a progeny population was raised for construction of a linkage map. Genotyping of the mapping population comprising the parents and 86 progenies was carried out using co-dominant SNP markers and dominant silico DArT markers derived from DArT sequencing (DArTseqTM). A linkage map with the DArTseq data was constructed using DArT PLs OCD MAPPING program, which implements a marker-ordering algorith combined with a tunable double cross-over masking algorith. Using the markers in common to join the two linkage maps, a consensus map was created which covered 3709 cM. A high density integrated genetic linkage map was constructed using 24004 markers, which assembled into 18 linkage groups, thus reflecting the haploid chromosome number of Hevea (n = 18). An average of 1334 markers per chromosome was observed with the markers spaced at an average inter marker distance of 0.15cM. Phenotyping for disease resistance to both P. meadii and C. cassiicola infections was carried out for the parents and 86 progeny population. In order to identify QTLs conferring resistance to these fungal diseases, genotypic and phenotypic data for disease resistance from the progeny population were merged to establish marker trait relationship for those traits. Six QTLs for Phytophthora disease resistance [fibe mapped in linkage group (LG) 9 and one in LG 15] and seven QTLs for Corynespora disease resistance (one each mapped in LG 6, 11, 13 and two each in LG 8 and 16) were identified at an adjusted P value cut off 0.001 and a LOD threshold score of 3.