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Identification and analysis of the whole genome of the marine-derived fungus <i>Penicillium brasilianum</i> HBU-136 revealed the presence of an interesting biosynthetic gene cluster (BGC) for non-ribosomal peptide synthetases (NRPS), highly homologous to the BGCs of indole-diketopiperazine derivatives. With the aid of genomic analysis, eight indole-diketopiperazines (<b>1</b>&#8722;<b>8</b>), including three new compounds, spirotryprostatin G (<b>1</b>), and cyclotryprostatins F and G (<b>2</b> and <b>3</b>), were obtained by large-scale cultivation of the fungal strain HBU-136 using rice medium with 1.0% MgCl₂. The absolute configurations of <b>1</b>&#8722;<b>3</b> were determined by comparison of their experimental electronic circular dichroism (ECD) with calculated ECD spectra. Selective cytotoxicities were observed for compounds <b>1</b> and <b>4</b> against HL-60 cell line with the IC₅₀ values of 6.0 and 7.9 &#956;M, respectively, whereas <b>2</b>, <b>3</b>, and <b>5</b> against MCF-7 cell line with the IC₅₀ values of 7.6, 10.8, and 5.1 &#956;M, respectively.