[Objective] Genetic diversity and relationship of 45 Ganoderma resinaceum strains from different areas in China were analyzed. [Methods] We studied clustering analysis and genetic diversity of these isolates using multi-gene analysis with ITS, TEF1-α, LSU sequences and SRAP technique. [Results] 8 pairs of primers on 45 strains were selected and amplificated using PCR-SRAP system, and 95 fragments were amplified, the number of polymorphic bands was 79, the average polymorphic rate was 82.4%. The PIC (polymorphism information content) value of these markers varied from 0.28 to 0.43, averaging 0.38. The results of multi-gene analysis with ITS, TEF1-α, LSU sequences and SRAP technique showed that part of the strains from the same area were clustered with each other, their kinship was close, and some strains with large gaps about the geographical distribution were also clustered in the same phylogenetic tree branch, their genetic relationship may also be relatively close, the result above was consistent with SRAP clustering analysis. [Conclusion] The genetic diversity of 45 strains was relatively abundant, and it had some correlation between genetic similarity and geographical distribution. ITS, TEF1-α and LSU sequences analysis and multi-gene analysis were more useful for classification and identification of Ganoderma resinaceum, and SRAP technique was more suitable for the genetic diversity analysis of Ganoderma resinaceum.