Blackheart is a physiological disorder induced by postharvest chilling storage during pineapple fruit export shipping. The aim of this study was to check the involvement of bromelain, the cysteine protease protein family abundantly present in pineapple fruits, and AcCYS1, an endogenous inhibitor of bromelain, in the development of blackheart. For this we checked the response to postharvest chilling treatment of two pineapple varieties (MD2 and Smooth Cayenne) differing in their resistance to blackheart. Quantitative RT-PCR analyses showed that postharvest chilling treatment induced a down-regulation of bromelain transcript accumulation in both varieties with the most dramatic drop in the resistant variety. Regarding AcCYS1 transcript accumulation, the varieties showed opposite trends with an up-regulation in the case of the resistant variety and a down-regulation in the susceptible one. Taken together our results suggest that the control of bromelain and AcCYS1 expression levels directly correlates to the resistance to blackheart development in pineapple fruits.