Fungal pigments, specifically those generated from spalting fungi, are being developed for broader use in the wood and textile industry, and due to their coloration properties, may also be useful as aesthetic bamboo dyes. This paper evaluates the potential use of fungal pigments in bamboo (Phyllostachys spp.), and compares the difference between natural spalting and the direct application of extracted fungal pigments of three known spalting fungi: Scytalidium cuboideum, Scytalidium ganodermophthorum, and Chlorociboria aeruginosa. Bamboo was significantly spalted by S. cuboideum under live inoculation, while the other two fungi did not colonize. For the direct application of fungal pigments, bamboo did not develop internal pigmentation with any pigment, but did develop visible surface color for S. cuboideium and C. aeruginosa. Light microscopy and scanning electron microscopy confirmed the presence of hyphae in bamboo vessels and parenchyma. An HPLC analysis for simple sugars showed the presence of glucose but no sucrose. Results indicate that the extracted pigments of the aforementioned fungi are ideal for the surface treatment of bamboo, while only direct inoculation of S. cuboideum is appropriate for internal coloration.