The tumor suppressor protein p53 restricts proliferation in response to DNA damage or the deregulation of mitogenic oncogenes, by leading to the induction of various cell cycle checkpoints, apoptosis or cellular senescence. Consequently, p53 mutations increase cell proliferation and survival and in some settings promote genomic instability and resistance to certain anti-cancer drugs. It is very important to identify chemotherapeutic agents that activate in a p53-independent manner for the development of treatments for p53-deficient tumors. Pectenotoxin-2 (PTX-2), isolated from marine sponges has been reported to display significant cytotoxicity to p53-deficient cancer cell lines. In this study, we compared the anti-cancer activity of PTX-2 in order to further test the status of p53 using two well-known hepatocarcinoma cell lines, p53-deficient Hep3B and p53-wild-type HepG2. MTT assay indicated that Hep3B cells were highly susceptible, whereas HepG2 cells were more resistant to this compound which was connected with the induction of apoptotic cell death in p53-deficient Hep3B cells, though not in HepG2 cells. The apoptosis induced by PTX-2 in Hep3B cells was associated with the down-regulation of anti-apoptotic Bcl-2 members (Bcl-2 and Bcl-xL) and IAP family proteins, the up-regulation of pro-apoptotic Bax protein and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-receptor 1/receptor 2 (DR4/DR5) and mitochondrial dysfunction. PTX-2 activated caspases (caspase-3, -8 and -9) and the blockade of caspase-3 activity by the caspase-3 inhibitor prevented the PTX-2-induced apoptosis in Hep3B cells. Additionally, the transcription factor early growth response-1 (Egr-1) gene was transcriptionally activated and the levels of non-steroidal anti-inflammatory drugs (NSAID)-activated gene-1 (NAG-1) protein were also elevated in PTX-2-treated Hep3B cells. Although further studies are needed to prove that an increased expression of Egr-1 by PTX-2 directly leads to NAG-1 induction and then apoptosis induction in p53-deficient Hep3B cells, the results of this study suggest that PTX-2 may be a good candidate for the development of a potential anti-tumorigenic agent in p53-deficient tumors.