Indonesia is one of the world’s leading producers of vanilla, an important cash crop for smallholders. Stem rot disease is a major constraint to vanilla production in Indonesia and has caused significant economic losses over the last decade. Previous reports of vanilla stem rots in the Asia-Pacific region include those caused by Fusarium, Colletotrichum and Phytophthora species. In this paper, we report Fusarium species associated with the disease. Seven major vanilla-producing provinces were surveyed for disease incidence and 850 samples were collected. Isolates were recovered from diseased stem tissues using a selective medium. Pure cultures on carnation leaf-piece agar and potato dextrose agar were identified based on morphological criteria. Some ambiguous species were verified based on DNA sequences of the translation elongation factor gene. A total of 542 Fusarium isolates were recovered, comprising 12 species, namely F. decemcellulare, F. fujikuroi, F. graminearum, F. mangiferae, F. napiforme, F. oxysporum, F. polyphialidicum, F. proliferatum, F. pseudocircinatum, F. semitectum, F. solani and F. subglutinans. F. oxysporum was the most commonly isolated species from all areas surveyed, followed by F. solani and F. semitectum. F. oxysporum, F. solani and F. semitectum were tested for pathogenicity to vanilla but only F. oxysporum was shown to be pathogenic. The vanilla stem rot pathogen in Indonesia is verified to be F. oxysporum f. sp. vanillae.
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