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• The genetic diversity was comprehensively evaluated based on morphological and SSR markers. • 49 out of 66 morphological characteristics presented coefficient of variation (CV) greater than 51%. • Seven main phenotypic components were able to justify 85.17% of total variance. • Growth potential was significantly correlated with flower sex, stigma length, grooves on fruit side, and sepal curl pose characters. • Bud sports, synonymous, and offspring persimmons could be successfully identified by morphological and SSR markers. Persimmon (Diospyros kaki Thunb.) is an economically important fruit crop that originates from China, and has been cultivated for thousands of years. However, the genetic variation remains largely unknown. Evaluation of agronomic traits and genetic diversity in different persimmon germplasm plays an essential role in understanding of the persimmon breeding application and efficient resource utilization. Herein, we carried out the comprehensive evaluation of genetic diversity of persimmon germplasm based on large-scale morphological traits, and SSR markers. A total of 242 accessions were evaluated using 66 phenotypic characteristics and 12 highly polymorphic SSR markers. The results showed that 28 out of 66 descriptive characteristics presented coefficient of variation (CV) greater than 40%, indicating the different accessions of persimmon had rich genetic diversity. Furthermore, it showed varying degrees of correlation among 66 morphological traits. Correlation coefficient analysis present that growth potential was significantly correlated with flower sex, stigma length, grooves on fruit side, and sepal curl pose characters. In addition, we extracted seven components with justifying 85.17% of total variance based on principal component analysis (PCA), and fruit-related traits were the most important variables in distinguishing accessions. Combined cluster analysis based on morphological traits and SSR markers, we identified the four accessions of bud sport, 48 persimmon of synonyms, and two varieties of offspring. This study sheds light on genetic variation of persimmon based on morphological and SSR markers, and provides a valuable resource for marker-assisted breeding of this important fruit crop. [ABSTRACT FROM AUTHOR]