The harmful alga Gymnodinium catenatum is one of the species that produces the neurotoxic, hydrophilic, tetrahydropurine derivatives known as paralytic shellfish toxins (PST). Studies have shown that several classes of marine toxins have genotoxic effects on bivalves. However, there are few studies on PST and their genotoxic effects on bivalves such as oysters. Experiments were performed to assess the effects of the toxic dinoflagellate G. catenatum on changes in the transcription level of the genes involved in cell-cycle regulation (p21, p53, cafp55) and initial inflammatory (casp1) processes and injuries in tissues of juvenile Crassostrea gigas. Our results reveal an effect at the level of transcription. The high transcription levels of the p21 and p53 genes found in oysters exposed to dinoflagellate diets suggest an activation of the cell-cycle checkpoints by DNA damage induction. At the histological level, the oysters exposed to the toxic dinoflagellate showed exfoliation, epithelial rupture and inflammation, which correlate with the observed changes in expression level of casp1 that is known to play a role in initial inflammatory responses. Our results provide molecular data suggesting probable DNA damage through expression modulation of the analysed key genes, in addition to histological evidence of tissue injuries due to PST dinoflagellate exposure.