We screened a colored clone from a metagenomic library derived from the marine sponge Halichondria okadai. We isolated a yellow pigment, halichrome A (1), which was structurally elucidated to be a biindole, exhibited cytotoxicity against B16 melanoma cells and was substituted with an ethyl group. To the best of our knowledge, this is the first report of the isolation of a novel compound from a metagenomic library derived from a marine sponge.