Paracoccidioidomycosis is an endemic fungal disease to Latin America caused by at least five species-level genotypes of Paracoccidioides, named P. lutzii, P. brasiliensis (S1a and S1b populations), P. americana, P. restrepiensis and P. venezuelensis. In spite of the clear association between armadillos and Paracoccidioides, just a handful of isolates of this fungus obtained from armadillos have ever been sequenced. Three P. brasiliensis, one P. americana (Sao Paulo, Brazil) and one P. restrepiensis (Caldas, Colombia) isolates derived from armadillos had their genomes fully sequenced. This paucity of genetic data from isolates from mammal reservoirs is particularly critical for the Amazon basin, one of the regions with the highest prevalence for PCM. Here we aim to bridge this gap by collecting Paracoccidioides isolates from armadillos from the Amazon and southern Brazil and comparing their genotypes to previously sequenced genomes.