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Fusarium wilt of banana (Musa spp.), caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most important banana diseases. Three races (1, 2, 4) of Foc have been identified worldwide, but race 4 (especially tropical race 4, TR4) is the most destructive pathogen and has significant impacts on banana production in Taiwan and Southern China. To characterize the genetic relationship of Foc in these two regions, 55 isolates of Foc, including 18 from Taiwan and 37 from Hainan and Guangdong Provinces, were subjected to pathogenicity tests, race 4-specific polymerase chain reaction (PCR) diagnosis, and amplified fragment length polymorphism (AFLP) analysis. One race 4 isolate from Australia, one race 1 isolate from Philippines, and 10 non-banana F. oxysporum isolates were also included in the study for comparison. Pathogenicity tests indicated that 16 and 21 isolates of Foc from Taiwan and Southern China, respectively, were pathogenic on Cavendish banana and classified as race 4, and the remaining isolates were identified as race 1. PCR amplification with race 4 and tropical race 4-specific primers confirmed that all of the race 4 isolates from Taiwan and Southern China were TR4. AFLP analysis with eight EcoRI-MseI primer combinations clustered the 67 F. oxysporum isolates analyzed into two major groups, one containing all race 4 isolates and the other consisting of race 1 isolates along with the non-banana F. oxysporum isolates. No significant divergence was observed among TR4 isolates from Southern China and Taiwan, suggesting that the TR4 isolates from Southern China might share the same lineage as those from Taiwan. [ABSTRACT FROM AUTHOR]