Cultivation of Cordyceps indigotica, an entomopathogenic fungus, in the presence of suberoyl bis-hydroxamic acid (an HDAC inhibitor) greatly activated its polyketide synthesis apparatus to afford six novel aromatic polyketides, indigotides C–F (1–4), 13-hydroxyindigotide A (5), and 8-O-methylindigotide B (6). The structures of these compounds were determined by NMR spectroscopic analyses. Among the compounds, indigotides C–E (1–3) possessed unprecedented dimeric polyketide frameworks possibly generated via a [4 + 2] cycloaddition or Michael type reaction.