Bacterial fruit blotch (BFB) is a severe seed-borne disease on melons. The type Ⅱ secretion system (T2SS), one of bacterial virulence factors, may contribute to bacterial colonization and transmission. In this study, genes encoding T2SS and the genetic organization of T2SS clusters in Acidovorax citrulli (Ac) strain AAC00-1 were compared with those in other plant pathogen species via KEGG and STRING databases. In addition, T2SS secretory proteins in Ac strain AAC00-1 with homology to experimentally proofed T2SS secretory proteins in other phytopathogenic bacteria were identified based on BLASTP search. The secretion signals, possibly involved metabolism pathways, presumed protein interaction, subcellular location in plant cells of T2SS secretory proteins in Ac strain AAC00-1 were analyzed. These results provide valuable information for further investigation of the underlying molecular mechanisms of the secretory proteins of Ac during the seed colonization and seedling transmission.