Abstract: 【Objective】 The objective of this project aims to make clear the distribution of the main pathogenic bacteria of cotton in northern Xinjiang and provide data for the establishment of cotton database, thus providing a basis for the effective prevention and control of diseases. 【Method】Four cotton main root and stem disease samples were collected from wide fields in 9 specimen collection areas of northern Xinjiang, using the pathogens specific primers of the 4 kind of main diseases (fusarium wilt, damping off, verticillium wilt red and rot) to carry out PCR detection of the diseases samples collected from northern Xinjiang. 【Result】The 4 kinds of pathogens were detected widely or more generally in the mixed samples from the 72 villages (or companies) of 9 specimen collection areas, but there were bigger difference in the detection rate among each pathogen. Among them, the detection rate of Fusarium oxysporum was higher, at 84.72%; and Rhizoctonia solani was the second, at 56.94%; while the detection rates of the Verticillium dahliae and Fusarium moniliforme were relatively low, at 45.83% and 37.50% respectively. 【Conclusion】These results showed that: F. oxysporum and fusarium wilt caused by it are the most common in all sampling areas, followed by R. solani and the disease caused by it. The two kinds of pathogens and the diseases caused by them are distributed in most villages in each sampling area; Verticillium dahliae and Verticillium dahliae are distributed in all sampling areas and nearly half of the villages. But, the distribution of F. moniliforme and red rot caused by it are not widely distributed, with obvious regional characteristics. Only higher frequency distribution is found in a few specimen collection areas.