Haploporus species have a worldwide distribution and 27 species have been accepted. In this study, two new species, Haploporus crystallinus and H. dextrinoideus, are proposed from South America, based on the molecular fragments (ITS, LSU and mtSSU) and morphological evidence. Molecular clock analysis was performed and the result suggests that the ancestor of Polyporales originated between the Late Jurassic and Early Cretaceous period, with a mean stem of 159.8 Mya [95% higher posterior density (HPD) of 142.4–184.1 Mya] and the genus Haploporus occurred at a mean stem of 108.3 Mya (95% HPD of 88.5–128.2 Mya). In addition, most species of the genus are diversified between 60.5 Mya and 1.8 Mya, during the Paleogene to Neogene. A key to the accepted species of the genus Haploporus is provided.