Topoisomerase IIalpha (top2) is a target of some of the most useful anticancer drugs. All clinically approved top2 drugs act to stabilize a drug-enzyme-DNA cleavable complex. Here we report the novel top2 activity of neoamphimedine, an isomer of the marine pyridoacridine amphimedine. Neoamphimedine was cytotoxic in yeast and mammalian cell lines. Neoamphimedine exhibited enhanced toxicity in top2 over-expressing yeast cells and was toxic in every mammalian cell line tested. However, neoamphimedine did not possess enhanced toxicity in a mammalian cell line sensitive to stabilized cleavable complexes. Therefore, we hypothesized that neoamphimedine is a top2-dependent drug, whose primary mechanism of action is not the stabilization of cleavable complexes. Top2-directed activity was determined in purified enzyme systems. Neoamphimedine-induced catenation of plasmid DNA only in the presence of active top2. This catenation correlated with the ability of neoamphimedine to aggregate DNA. Catenation was also observed using a filter-binding assay and transmission electron microscopy. Catenation was confirmed when only restriction enzyme digestion could resolve the catenated plasmid complex to monomer length plasmid DNA. Neoamphimedine also showed potent anti-neoplastic activity in human xenograft tumors in athymic mice. Neoamphimedine was as effective as etoposide in mice bearing KB tumors and as effective as 9-aminocamptothecin in mice bearing HCT-116 tumors. Amphimedine did not induce DNA aggregation or catenation in vitro, nor did it display any significant anti-neoplastic activity. These results suggest that neoamphimedine has a novel top2-mediated mechanism of cytotoxicity and anticancer potential.