The genus Ganoderma belongs to Polyporales, well-known for its medicinal properties and as a plant pathogen. The aim of this study was to identify the genetic variation between populations of two Ganoderma lucidum Karst. complex isolates using RAPD. For this purpose, four populations of G. resinaceum Boud. and eight populations of G. lucidum collected and purified during 2011-2012, were studied for the first time in Iran. Ten random primers were used for RAPD reaction. The result for RAPD-PCR studies of G. lucidum complex showed a wide range of diversity, as scores of 61.48 and 40.16 were estimated for the inter-specific diversity of G. lucidum and G. resinaceum, respectively. Cluster analysis confirmed the separation of two species populations in different clusters. In the analysis of genetic structure, two probable groups (K = 2) were identified in the studied germplasm which was also confirmed by the results of bar plot.