Paracoccidioides brasiliensis is a temperature-dependent dimorphic fungus and the agent of paracoccidioidomycosis (PCM), which is prevalent in rural workers of Latin American countries. Until a decade ago, most of the studies involving P. brasiliensis used clinical isolates, since environmental samples from soil are difficult to obtain. More recently, P. brasiliensis has been isolated from infected wild and domestic animals, especially from the nine-banded armadillo Dasypus novemcinctus in Brazil. Over the years, diversity within the species has been observed at several phenotypic levels. The present review will discuss the reports focusing on genetic polymorphism, which culminated with the detection of P. brasiliensis phylogenetic species as a result of a multilocus study. Polymorphism in the PbGP43 gene is detailed. This gene encodes fungal glycoprotein gp43, a dominant P. brasiliensis antigen largely studied in the last two decades for its importance in diagnosis, immune protection, and adhesive properties to extracellular matrix-associated proteins. Fungal traits associated with genetic groups are discussed.