Sequence data from the article: Complete genome assemblies of several Xylella fastidiosa subspecies multiplex strains reveals high phage content and novel plasmids. In this study, we present the complete genome sequences of twelve strains of Xylella fastidiosa, a bacterial plant pathogen that has spread throughout the Americas, as well as in various European countries. These strains were isolated from different plant hosts, including Olea europaea (XYL1966/18, XYL466/19, and XYL468), Prunus sp. (CFBP8070, CFBP8075, CFBP8173, XF3348, and XYL1752/17), Santolina chamaecyparissus (Santa29b), Spartium junceum (CFBP8417, and CFBP8418), and Ulmus sp. (CFBP8068). We used a combination of long and short-read technologies for whole genome sequencing, and the taxonomic assignment at the subspecies level was determined through MLST analysis, which involved seven housekeeping genes (Yuan et al., 2010)