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[Objectives] The study was to identify the casual agent of freckle disease on Cavendish banana in Hainan Province, China. [Methods] Fungal isolates were isolated from affected lea tissues and identified by the morphological features, molecular identification and pathogenicity test. [Results] The fungus isolated from affected lea tissues was identified as Phyllosticta capitalensis based on the morphological properties of the colony and spore, coupled with sequence analyses of the interna transcribed spacer (ITS) region and the large subunit (LSU) rDNA gene. Koch's postulates were fulfilled by successfully re-isolating the pathogen from the artificial inoculated leaves. [Conclusions] P. capitalensis is a new pathogen responsible for Cavendish banana freckle disease in Hainan. [ABSTRACT FROM AUTHOR]