The invention discloses a histology method for early detection of latent Botryosphaeria dothidea in apple fruit, and relates to the field of detection of pathogenic bacteria in plant tissues. The method is applicable to for survey of quantity of lenticels latent with Botryosphaeria dothidea in apple fruit. The specific method is as below: boiling apple fruit or fruit tissue to be detected at a temperature of no lower than 100 DEG C for more than 10 minutes, and stripping the skin; clarifying the stripped skin by 1%-15% sodium hypochlorite for 5-20 minutes, soaking in 1%-30% potassium hydroxide or sodium hydroxide for 3-5 minutes, staining with 0.1%-3% aniline blue water solution for 3-5 minutes, and making a temporary slide with 20%-80% glycerol as a floating carrier; illuminating with UV of 315nm-400nm under a fluorescence microscope, observing mycelia coated by the suberification tissue inner surface of lenticels, so as to determine whether the lenticels are infected by Botryosphaeria dothidea. The invention solves the problem of timely detection of infection amount of Botryosphaeria dothidea in the research of the Botryosphaeria dothidea in fruit, and provides a simple and reliable technical method for the early detection of the infection amount of Botryosphaeria dothidea.