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For exploring structurally diverse metabolites and uniquely metabolic mechanisms, we systematically investigated the chemical constituents and putative biosynthesis of <i>Janibacter</i> sp. SCSIO 52865 derived from the deep-sea sediment based on the OSMAC strategy, molecular networking tool, in combination with bioinformatic analysis. As a result, one new diketopiperazine (<b>1</b>), along with seven known cyclodipeptides (<b>2</b>–<b>8</b>), <i>trans</i>-cinnamic acid (<b>9</b>), <i>N</i>-phenethylacetamide (<b>10</b>) and five fatty acids (<b>11</b>–<b>15</b>), was isolated from the ethyl acetate extract of SCSIO 52865. Their structures were elucidated by a combination of comprehensive spectroscopic analyses, Marfey’s method and GC-MS analysis. Furthermore, the analysis of molecular networking revealed the presence of cyclodipeptides, and compound <b>1</b> was produced only under mBHI fermentation condition. Moreover, bioinformatic analysis suggested that compound <b>1</b> was closely related to four genes, namely <i>jat</i>A–D, encoding core non-ribosomal peptide synthetase and acetyltransferase.