Ganoderma lucidum has been found to be a pathogen on a wide range of tree species in India. Because of large variations found in both macro- and microscopic characters, traditional identification and characterization methods are unreliable for this genus. We analysed nrDNA internal transcribed spacer (ITS) sequences of 52 isolates in the G. lucidum complex by the parsimony method, finding 17 lineages. The maximum parsimony analysis showed that the isolates of G. lucidum from the same host species had high similarity in ITS sequences, compared to isolates from other tree species. The result was also supported by high values of population differentiation parameters such as NST and FST values. Genetic analysis suggests the occurrence of host-mediated genetic differentiation in G. lucidum isolates, which requires further investigation.