From the ethyl acetate extract of the bacterial strain Cytophaga sp. AM13.1, among many known compounds, the new natural products 2,5-bis(3-indolylmethyl)pyrazine (2) and a highly symmetrical p-cyclophane named pharacine (5) were identified. In addition, tryptamine isovalerate (1) and p-hydroxyphenylacetamide (4), known as plant metabolites, were isolated and characterized from a microorganism for the first time. The new natural products showed no activity against three microalgae, the fungus Mucor miehei, the yeast Candida albicans, and the bacteria Staphylococcus aureus, Bacillussubtilis, Escherichia coli, and Streptomyces viridochromogenes.