Coniophora eremophila and Antrodia sinuosa cause brown heartrot in living lemon trees in southern Arizona and California. They can be distinguished in the field by differences in rot characteristics. Both have a high optimum growth temperature of approximately 35°C. Coniophora eremophila has a cultural morphology typical of other Coniophora species and did not fruit in culture. Antrodia sinuosa cultures were morphologically similar to previous reports and fruited readily under laboratory conditions. Mating tests with homokaryotic single spore isolates showed it to have a heterothallic bipolar mating system. The decay capacity of C. eremophila on lemon wood test blocks under laboratory conditions was low compared to that of A. sinuosa, five other brown rot fungi, and three white rot fungi.