Dynamic changes of fungi population were analyzed by tissue isolation on leaves, flower clusters and fruits in litchi. Fourteen genera of fungi were isolated, including 11 pathogenic fungi and 3 nonpathogenic fungi. Colletotrichum sp. and Phomopsis sp. belonged to resident population on litchi old leaves, flower clusters and fruits. In old leaves, isolation Cytospora sp. was resident all the year, and its isolation frequency was 43.7%. Alternaria sp. and Cladosporium sp. widely distributed at the stage of blossom and fruit bearing. The precipitation of Maoming in 2009 was 1 396.9 mm. There was a positive correlation between isolation frequency of Alternaria sp. and the daily mean rainfall in flower clusters and fruit stalks with 0.2-12.4 mm precipitation range, their one-dimensional linear regression equation was y=11.99+2.5 x (r²=0.99，P< 0.01), while there was no correlation between daily mean rainfall and isolation frequency of Colletotrichum sp., Phomopsis sp., Cladosporium sp. and Geotrichum sp.. There were maximum pathogenic fungi at the second physiological drop and during fruit maturation, while the isolation frequency was the lowest at the last fruit-drop before harvest. The rainfall and other factors together affected distribution of pathogenic fungi.