Phenotypic traits (physiological characteristics and somatic incompatibility) and genotypic traits (target region amplification polymorphism TRAP) were used to survey the diversity in Chinese Auricularia auricula systematically, which consisted of 32 main cultivated strains. The 27 important and stable physiological indexes were evaluated; somatic incompatibility test (SIT) reaction was described from three aspects: type, pigment, and intensity while intensity clustering alone revealed the phenotypic diversity among the 32 strains;16 pairs of TRAP primer combinations produced 535 unambiguous and reproducible DNA fragments, of these 524 (97.9%) were polymorphic. The phylogenetic trees were constructed by Unweighted Pair-group Method with Arithmetic Averages (UPGMA), which distributed the test strains into four to six major groups respectively. The principal coordinate analysis (PCO) of the three methods (physiological characteristics, SIT intensity and TRAP) exhibited highly similar clustering patterns, revealing that all the test strains can be divided into three groups considered significantly correlated with geographical regions. Results revealed the occurrence of relatively low diversity of A. auricula in the study. The cultivated strains in the same region are more similar physiologically and some strains are suspected to be synonymous. This study suggests that the value for estimating diversity are represented by TRAP＞SIT reaction intensity＞physiological characteristics in A. auricula, and PCO analysis can provided more effective and visible information than the UPGMA clustering dendrogram. Our finding will facilitate future germplasm resources management and breeding program of A. auricula in China.