Piper tuberculatum is an exotic Piper from the Amazon region that shows resistance to infection by Fusarium solani f. sp. piperis, causal agent of Fusarium disease in black pepper (Piper nigrum L.). In this work we aimed to study the interaction between P. tuberculatum and F. solani f. sp. piperis at a molecular level, using suppression subtractive hybridization to identify genes potentially related to Fusarium disease resistance. Comparative sequence analysis confirmed that clones isolated here show a high identity with genes coding for proteins that have a known role in plant defense response mechanisms, such as peroxidase, hydroxyproline-rich glycoprotein and CBL-interacting protein kinase. The present study constitutes the first effort to understand the molecular basis of this plant-pathogen interaction, identifying genes which may be used in the future genetic improvement of black pepper.