Gamma-linolenic acid methyl ester (methyl GLA) was purified from the cultures of Rhizopus oryzae KSD-815, which is a filamentous fungus and has been used to make Korean traditional alcoholic beverage. In the present study, molecular mechanisms by which methyl GLA induces apoptosis in human prostate cancer cells, LNCaP, were investigated. It was found that methyl GLA mediated-apoptosis was provoked by down-regulation of mammalian target of rapamycin (mTOR) pathway, resulting from activation of AMP-activated protein kinase (AMPK) pathway and inactivation of Akt. On the other hand, a marked increase of p38 mitogen-activated protein kinase (MAPK) phosphorylation was observed within 30 min after methyl GLA treatment. Although p38 MAPK specific inhibitor, SB203580, completely blocked caspase-9 activation but not caspase-8, p38 MAPK activation was not affected by the broad caspase inhibitor, Z-VAD-FMK, which nevertheless prevented methyl GLA-provoked apoptosis. Interestingly, interference of methyl GLA-mediated p38 MAPK with SB203580 attenuated inactivation of mTOR, independent of AMPK pathway. Results indicate that methyl GLA can independently utilize two different signaling pathways for inducing the apoptosis cascade, and p38 MAPK activation is a specific regulatory role in methyl GLA-provoked apoptosis, enhancing the action mechanisms by fermentation metabolites to regulate cell death.