The xylem limited plant pathogenic bacterium Xylella fastidiosa causes economically important diseases on agronomic, horticultural and landscape plants. This review includes the current status of polymerase chain reaction (PCR) based systems for detection and characterization of X. fastidiosa, and presents a genome-wide analysis of strain differentiation. The use of genomics data for strain comparisons will improve the understanding of the genetic determinants of strain specific pathogenicity and virulence. The genome-level analysis can be applied to design new strategies for management and control of Xylella fastidiosa associated diseases in a wide range of crops.