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[Objectives] This study was conducted to determine the pathogen species and dominant species of sugarcane pokkah boeng in the sugarcane areas of Yunnan in the low-latitude plateau, so as to provide a basis for the pathogenic mechanism, disease resistance breeding and scientific prevention and control of pokkah boeng. [Methods] With 14 pokkah boeng samples collected from different sugarcane areas in Yunnan as materials, pokkah boeng-specific detection primers Fv-F4/Fv-R4 and Fp-F3/Fp-R3 were designed based on ribosomal DNA non-transcribed spacer (rDNA-ITS) sequences, respectively, and used to perform PCR on Fusarium, verticillioides and F. proliferatum. [Results] In 12 of the 14 pokkah boeng samples, two species of pokkah boeng pathogens were detected, and there was a phenomenon of composite infection. Seven composite infection samples were selected for sequence alignment and phylogenetic analysis. The sequences of F. verticillioides (GenBank accession number; MZ126549-MZ126555) and F. proliferatum (GenBank accession number; MZ102259-MZ102265) from seven composite infection samples shared 98.6% -100% and 100% with F. verticillioides strain 20 (GenBank accession number; KU508286) and F. proliferatum Dehong strain (GenBank accession number; KJ629482) published in GenBank, respectively. The phylogenetic tree showed that the pathogens of sugarcane pokkah boeng in Yunnan were mainly divided into the F. 'verticillioides group and F. proliferatum group. In the F. 'verticillioides group, except for ROC 25 (Lancang, Yunnan) and Funong 10-1405 (Maitreya, Yunnan) which were on an independent branch, the remaining five composite infection samples were grouped with F. verticillioides strains from different geographical origins, and were closely related to F. oxysporum Guangxi strain. All strains of F. proliferatum from different geographic origins were clustered into another group. [Conclusions] This study provides a scientific basis for disease resistance breeding and disease prevention and control of sugarcane pokkah boeng. [ABSTRACT FROM AUTHOR]