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Ganoderma lucidum is an interesting shelf fungus that is also of medical importance in East Asian countries such as China, Japan and Korea. The fruit bodies of different Ganoderma species have similar colors and shapes, but are different regarding their medicinal properties. In order to provide molecular evidence for the genuine origin of G. lucidum, G. sinense and G. tsuga, fungal immunomodulatory protein (FIP) genes were cloned using genomic walker technology and their sequences were then determined. Based on the sequences of cloned FIP genes, we designed three pairs of species-specific primers for amplification and sequencing of FIP genes. These new primers allowed an effective amplification and sequencing of FIP genes from representative species of G. lucidum, G. sinense and G. tsuga. Phylogenetic relationships were resolved quite efficiently by the FIP gene sequences, which proved to be more useful than other genetic marker techniques in phylogenetic reconstruction of G. lucidum, G. sinense and G. tsuga.