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[Objective] The nucleotide sequences of rDNA-ITS and large subunit of Ceratocystis paradoxa (de Seynes) Moreau causing sugarcane pineapple disease, were analyzed in order to provide technological supports for rapid and effective molecular detection of the pathogen in sugarcane production. [Method]A representative strain FL-1 was isolated from R0C22 underground seedcane with pineapple disease. The pathogenicity of strain FL-1 to sugarcane plants was determined by artificial inoculation based on Koch's postulates. The morphological characteristics of FL-1 colony grown on PDA medium were observed, as well as its conidiophores, aleurioconidia and conidia under light microscope. The nucleotide sequence regions of rDNA-ITS and large subunit were amplified by using primers ITS1/4 and NL1/4. The phylogenetic tree based on ITS and large subunit sequences of strain FL-1, respectively, were constructed by using Neighbor-joining method, and their phylogenetic distance were analyzed using the p -distance program in software MEGA. [Result]The isolate FL-1 was determined as the pathogen causing sugarcane pineapple disease ac-cording to the pathogenicity test, and it was charactered by typical arthrospores and aleurioconidia, which was consisted with that of C. paradoxa. The nucleotide sequences of rDNA -ITS and large subunit amplified from genome DNA of isolate FL-1 were 499 and 563 bp in length, respectively. And they shared 100.0% of homology with the fungus of C. paradoxa. The rDNA-ITS sequence was clustered with C. paradoxa in an absolute evolution group in the phylogenetic tree, as well as the large subunit sequence. The genetic distance matrix results showed that rDNA-ITS and large subunit sequences of isolate FL-1 were genetically clustered with C. paradoxa, and the intraspecific genetic distance were 0-0.017 and 0-0.008, respectively. While, the interspecific genetic distance of Ceratocystis were 0.015-0.106 and 0.002-0.059, respectively. Therefore, FL-1 strain was identified as C. paradoxa based on morphological characteristics and molecular detection. [Conclusion]The isolate FL-1 from sugarcane was considered as member of the C. paradoxa complex and primarily classified into the Clade 1 of complex. rDNA-ITS and large subunit were fit for PCR detection and molecular marker of sugarcane pineapple disease. [ABSTRACT FROM AUTHOR]