Ovarian cancer (OC) often metastasizes to the peritoneal cavity, causing late-stage diagnosis with high mortality. Aaptamine and isoaaptamine, sponge-derived isomeric alkaloids, were investigated for the anti-tumor potential of isoaaptamine in OC cells. Isoaaptamine outperforms aaptamine, significantly reducing the viability of PA-1 and SKOV-3 cells with half maximal inhibitory concentration (IC