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Chemical investigations of <i>Aquimarina</i> sp. MC085, which suppressed TGF-β-induced epithelial–mesenchymal transition (EMT) in A549 human lung cancer cells, led to the isolation of compounds <b>1</b>–<b>3</b>. Structural characterization using spectroscopic data analyses in combination with Marfey’s analysis revealed that they were two diketopiperazines [<i>cyclo</i>(<span style="font-variant: small-caps;">l</span>-Pro-<span style="font-variant: small-caps;">l</span>-Leu) (<b>1</b>) and <i>cyclo</i>(<span style="font-variant: small-caps;">l</span>-Pro-<span style="font-variant: small-caps;">l</span>-Ile) (<b>2</b>)] and one N-phenethylacetamide (<b>3</b>). <i>Cyclo</i>(<span style="font-variant: small-caps;">l</span>-Pro-<span style="font-variant: small-caps;">l</span>-Leu) (<b>1</b>) and N-phenethylactamide (<b>3</b>) inhibited the TGF-β/Smad pathway and suppressed the metastasis of A549 cells by affecting TGF-β-induced EMT. However, <i>cyclo</i>(<span style="font-variant: small-caps;">l</span>-Pro-<span style="font-variant: small-caps;">l</span>-Ile) (<b>2</b>) downregulated mesenchymal factors via a non-Smad-mediated signaling pathway.