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Background  The  Dickeya  genus is part of the  Pectobacteriaceae  family that is included in the newly described  enterobacterales  order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution and host range. Among them, the new  Dickeya fangzhongdai  species groups causative agents of maceration-associated diseases that impact a wide variety of crops and ornamentals. It affects mainly monocot plants, but  D. fangzhongdai  strains have also been isolated from pear trees and water sources. Here, we analysed which genetic novelty exists in this new species, what are the  D. fangzhongdai -specific traits and what is the intra-specific diversity.    Results  The genomes of eight  D. fangzhongdai  strains isolated from diverse environments were compared to 31 genomes of strains belonging to other  Dickeya  species. The  D. fangzhongdai  core genome regroups approximately 3500 common genes, including most genes that encode virulence factors and regulators characterised in the  D. dadantii  3937 model strain. Only 38 genes are present in  D. fangzhongdai  and absent in all other  Dickeyas . One of them encodes a pectate lyase of the PL10 family of polysaccharide lyases that is found only in a few bacteria from the plant environment, soil or human gut. Other  D. fangzhongdai -specific genes with a known or predicted function are involved in regulation or metabolism.  The intra-species diversity analysis revealed that seven of the studied  D. fangzhongdai  strains were grouped into two distinct clades. Each clade possesses a pool of 100–150 genes that are shared by the clade members, but absent from the other  D. fangzhongdai  strains and several of these genes are clustered into genomic regions. At the strain level, diversity resides mainly in the arsenal of T5SS- and T6SS-related toxin-antitoxin systems and in secondary metabolite biogenesis pathways.    Conclusion  This study identified the genome-specific traits of the new  D. fangzhongdai  species and highlighted the intra-species diversity of this species. This diversity encompasses secondary metabolites biosynthetic pathways and toxins or the repertoire of genes of extrachromosomal origin. We however didn’t find any relationship between gene content and phenotypic differences or sharing of environmental habitats.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5332-3) contains supplementary material, which is available to authorized users.

Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates