Aims: The objective of this study is to identify the causal agent of a new fruit rot disease on jackfruit which was observed in the jackfruit-growing area in Taman Kekal Pengeluaran Makanan (TKPM), Pahang State of Malaysia in late 2016. The disease has been continuously spreading and caused huge economic loss to jackfruit farmers in Malaysia. Methodology and results: Bacterial strains isolated from the disease plant were preliminary identified using basic morphological and physiological test and confirmed by polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene. The isolates from infected tissue were Gram-negative and motile rods bacteria producing circular, mucoid colonies on LB medium that are 2 mm wide after 48 h at 28 °C. It appeared creamy to white in colour on NA medium with more watery consistency. The 16S rRNA was amplified for the isolated strains and sequences were compared with the NCBI database using BLAST. The results showed 97 to 99% identity similarity to Dickeya fangzhongdai, strain JS5 (accession no. KT992690). Phylogenetic analysis indicated that the isolates from this study were clustered together in the clade of D. fangzhongdai. Sequence data from isolated strains were deposited in GenBank (accession no. MH197139, MH842152 and MH842153). Characteristic symptoms of fruit rot disease appeared after 2 days of post inoculation though Koch’s postulate. Conclusion, significance and impact of study To the best of our knowledge, this is the first report of a new bacterial fruit rot disease of jackfruit caused by species of Dickeya in Malaysia. The bacterium is now considered as one of several bacterial causing diseases which impacted major loses of jackfruit industry in Malaysia.