We explored evolutionary relationships within the Lyophyllaceae by combining sequence data from six loci. The most likely phylogram led us to reconsider the Lyophyllaceae classification with the recognition of two new genera (Myochromella and Sagaranella) based on ecological and/or morphological distinctiveness. Lyophyllaceae are ecologically highly diversified and our phylogeny suggests that four to five ecological transitions from free-living to parasitic or mutualistic lifestyles have occurred within the family. Due to moderate phylogenetic support recovered for several relationships within that clade and due to the uncertainty about the ecological strategy adopted by five of the sampled species, three out of these transitions could be unequivocally reconstructed suggesting that saprotrophy is plesiomorphic for Lyophyllaceae. Significant differences in rates of molecular evolution were detected among taxa. These differences are not associated with ecological transitions throughout the Lyophyllaceae, however, within each of the major clades identified in the family, taxa of different ecological strategies show an overall tendency to evolve at different speeds at the molecular level.