Most of the research related to Peruvian Amazon fungi is focused on edible mushrooms and pathogens. Other important fungi, such as the spalting type (decay fungi that pigment wood internally), are not broadly studied, as most of them do not produce fruiting bodies and can be difficult to locate. Spalting fungi, however, are of broad economic importance due to their ability to produce pigments that enhance wood aesthetics, resulting in an increased economic value. In order to begin understanding the diversity of spalting fungi within certain regions of the Amazon, a sampling of downed trees and branches (through the opening of the xylem to identify potential pigmenting and zone line producing fungi) was done in the district of Las Piedras, Madre de Dios, Peru. Fungi suspected of causing internal pigment and zone lines were collected, cultured, isolated, and sequenced. The species found belonged to the orders Helotiales, Xylariales, Hypocreales, Russulales, Polyporales, Botryosphaeriales and two specimens of the class Leotiomycetes. The fungi collected produced pigments or zone lines in wild conditions and all of them were capable of wood decomposition. Interestingly, these are the same orders and genera as North American spalting fungi, which may indicate a correlation within species that pigment wood. The results obtained start a specific database of spalted fungi in the Amazon and, with it, help support an effort to increase the forest value of ecosystems primarily used for a few high-valued tree species.