Abstract In this report, we assess by suppression subtractive hybridization (SSH) the biological process of the South American leaf blight (SALB) that is an important disease of rubber tree caused by Microcyclus ulei (P. Hem.) v. Arx. Leaves from MDF180 (a partially resistant cultivar from Peruvian origin) and PB314 (a susceptible cultivar) were inoculated with M. ulei . Leaf fragments were collected from 6 h post-infection (hpi) to 58 days post-infection (dpi) and five cDNA libraries enriched for genes induced by M. ulei in order to identify up-regulated genes at the different stages of the host-parasite interaction. We sequenced 8027 expressed sequence tags (EST). After control of their quality, trimming and assembling, we obtained 1165 singlets and 458 contigs. The EST redundancy within each SSH library varied from 23% to 87%. Based on sequence similarity 49% of the sequences could be assigned to functional categories, whereas 21% corresponded to unknown function and 30% did not show any significant similarity with other sequences. The profile of gene expression was different for each library and gave a comprehensive picture of the transcriptome dynamics of rubber tree in response to M. ulei throughout the infection process. Most of the ESTs described in this study (80%) are specific to leaf tissues since they did not show any homology with ESTs previously identified in latex transcriptome. The occurrence of ESTs whose functional annotation was related to “stress” or “defence” was compared between libraries and their specific function is discussed in relation to the corresponding stage of leaf lesions and to histological observations. As far as we known, this is the first report on ESTs from Hevea brasiliensis collected during a biotic stress. It provides a significant contribution to the understanding of the molecular mechanism of the resistance and the susceptibility to South American leaf blight and it represents a new molecular resource for the development of polymorphic markers and marker-assisted selection.