Boid Inclusion Body Disease (BIBD) is a transmissible viral disease of captive snakes that causes severe losses in snake collections worldwide. It is caused by reptarenavirus infection, which can persist over several years without overt signs, but is generally associated with the eventual death of the affected snakes. Thus far, reports have confirmed existence of reptarenaviruses in captive snakes in North America, Europe, and Australia, but there is no evidence that it also occurs in wild snakes. BIBD affects both boas and pythons, the habitats of which do not naturally overlap. Herein, we studied Brazilian captive snakes with BIBD using a metatranscriptomic approach, and report the identification of novel reptarenaviruses, hartmaniviruses, and a new species in the family Chuviridae. The reptarenavirus L segments identified represent six novel species, while we only found a single novel reptarenavirus S segment. Until now, hartmaniviruses had been identified only in European captive boas with BIBD, and the present results increase the number of known hartmanivirus species from four to six. The newly identified chuvirus showed 38.4%, 40.9%, and 48.1% amino acid identity to the nucleoprotein, glycoprotein, and RNA-dependent RNA polymerase of its closest relative, Guangdong red-banded snake chuvirus-like virus. Although we cannot rule out the possibility that the found viruses originated from imported snakes, the results suggest that the viruses would circulate in indigenous snake populations.