The eight isolates belonging to the FFSC were further analysed using a multi-gene phylogeny based on cmdA, rpb1, rpb2, tef1, and tub. The final alignment included 4 795 characters (cmdA 545, rpb1 1534, rpb2 1551, tef 677 and tub 488) including align- ment gaps, and encompassed 54 isolates, with two outgroup taxa (F. oxysporum CBS 716.74 and CBS 744.97) (Table 2).

The analysis was consistently able to distinguish the three biogeographical clades known as the African,American and Asian clades sensu O’Donnell et al. (1998 a). All of the Indonesian isolates clustered within the Asian clade of FFSC except for isolate InaCC F 991, identified as F. verticilloides, and clustered within the African clade (Fig. 2). According to the multi-gene analysis, two isolates (InaCC F 962 and InaCC F 992) were identified as F. proliferatum, while two new phylogenetic species were recognised among the Indonesian isolates. Isolates InaCC F 872 and InaCC F 993, from central and East Java, respectively, clustered in a distinct, highly supported clade (96 bs/0.99 pp) closely related to F. mangiferae. Isolates InaCC F 950–152, formed a distinct group (100 bs/1.0 pp), closely related to, but genetically distinct from F. sacchari.