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Abstract Pestalotiopsis and related genera, including Neopestalotiopsis and Pseudopestalotiopsis have damaged many plants for many decades; however, there is little available information about the fungi on tropical fruit in Thailand. This study isolated and characterized pestalotioid fungi on tropical fruit, investigated host specificity, and screened whether plant extracts could control the fungi. In total, 53 diseased fruit samples were sampled from eight types of fruit trees (jackfruit, rose apple, mangosteen, plum, snake fruit, rambutan, strawberry, and avocado). Based on morphological characteristics, 44 isolates were classified as belonging to pestalotioid taxa. Of these isolates, seven with distinct characteristics were selected for identification using molecular analysis, and six isolates were identified as Neopestalotiopsis and one as Pseudopestalotiopsis. In the cross-inoculation experiment, the isolates exhibited nonhost specificity and could infect at least two host plants. The isolates were used to screen for a potential biocontrol resource using six crude plant extracts (clove, ginger, lemongrass, mangosteen, roselle, and turmeric). All crude extracts except mangosteen could inhibit the growth of Neopestalotiopsis and Pseudopestalotiopsis. Application of crude plant extracts could be a potential treatment to control these diseases on tropical fruit.