Currently, gall rust is the most important disease of Falcataria moluccana in Indonesia. The gall rust pathogen was identified as Uromycladium falcatariae, in a recent study using molecular approaches. However, the molecular study of the F. moluccana gall rust pathogen from Indonesia has not been reported. Therefore, the study aimed to analyse this through molecular phylogenetic of the internal transcribed spacer‐5.8S rDNA (ITS), the cytochrome oxidase 3 (CO3) gene and the gene encoding the large ribosomal subunit (LSU) as well as analyses of its spore dimensions and number of striae. For this purpose, isolates of the gall rust pathogen of F. moluccana were collected from three provinces in Java and one province in Sumatra. The average of spore lengths and the widths varies, with the isolate from Bengkulu, having the largest spore dimension. For the number of striae, isolate from Central Java had a wider range compared with other isolates. Phylogenetic analysis of ITS, LSU and CO3 sequences using maximum likelihood revealed a genetically distinct group of the gall rust pathogen of F. moluccana originating from the various provinces in Indonesia with isolates from the Philippines and Timor Leste. The gall rust pathogens may have evolved to adapt to a populations of F. moluccana in Java.