In this study, metagenomic analysis was employed to investigate the bacterial communities in the Muan tidal mudflat of the Republic of Korea. We used metagenomic analysis to identify the microbial community in tidal soil dominated by Proteobacteria. From this environment, the bacterial strain, sp. CMS18, was isolated and yielded two previously unknown compounds, penipaline D () and -acetyl-dimethylallyltryptophan (). The chemical structures of the isolated compounds along with 6-dimethylallyl-indole (), 6-dimethylallyltryptophan (), penipaline D (), and -acetyl-dimethylallyltryptophan () were structurally investigated using HR-ESI-MS and NMR spectroscopy. The isolated compound 6-dimethylallyl-indole () demonstrated broad-spectrum antifungal activity, with IC value of 0.04 mM against and 0.35 mM against both and . Additionally, it exhibited additive interaction with caspofungin against .