Integrating MS-based metabolomics approaches, LC-MS-PCA and molecular networking enabled the targeted isolation of five new pyrrole-derived alkaloids, phallusialides A-E (<b>1</b>-<b>5</b>), from a marine-derived <i>Micromonospora</i> sp. bacterium. The structures of <b>1</b>-<b>5</b> were elucidated by analysis of their HRMS, MS/MS, and NMR spectroscopic data. The absolute configuration of phallusialide A (<b>1</b>) was determined on the basis of comparisons of experimental and theoretically calculated ECD spectra. Compounds <b>1</b> and <b>2</b> exhibited antibacterial activity against methicillin resistant <i>S. aureus</i> (MRSA) and <i>E. coli</i>, with MIC values of 32 and 64 μg/mL, respectively, whereas <b>3</b>-<b>5</b> showed no antibacterial activity even at 256 μg/mL, yielding important SAR insights for this class of compounds.