Tissue isolation and purification of the diseased fruit of ‘Ehime 38’ were carried out, pathogen strains AY-11 and GP-1 were obtained, through traditional morphology and molecular biology(ITS, LSU, TUB2 and EF-α) identification methods, the pathogen strains AY-11 and GP-1were identified as Lasiodiplodia pseudotheobromae and Lasiodiplodia theobromae respectively. Pathogenicity test carried on healthy citrus fruits showed the two pathogen strains caused fruit rot on the citrus, and Lasiodiplodia pseudotheobromae and Lasiodiplodia theobromae were recovered from the lesion organs, confirming strains AY-11 and GP-1 as the primary pathogens. The pathogenicity test carried on different varieties of citrus showed that the two strains had strong pathogenicity to these varieties of citrus including ‘Italian lime’, ‘Moroccan lime’, ‘Ehime 38’, ‘Harumi’ and ‘Goutoucheng’, forming brown watery round spots on branches, leaves and fruits, of which the largest spots were seen in Harumi. Indoor screening of fungicides using mycelial growth rate method showed that among the 21 agents, 40% Carbendazim WP showed the strongest inhibitory effect on strain AY-11, with EC50 of 0.025 μg/mL. And 29% Isopyrazam?Azoxystrobin SC showed the strongest inhibitory effect of strain GP-1, with EC50 of 0.023 μg/mL. Field tests showed that and 45% Prochloraz water emulsion diluted 1000 times, 75% Oxime bacteria Tebuconazole water dispersible granules diluted 5000 times, 70% Thiophanate methyl wettable powder diluted 800 times and 25% Pyrazolidonil EC diluted 1000 times all showed 100% prevention effects, indicating these fungicides can reduce the rotten fruit rate and effectively prevent and control the disease.