2006 Annual Report 4d.Progress report. This report documents research conducted under a reimbursable agreement between ARS and California Department of Food and Agriculture. Additional details of the research can be found in the report for the parent project 5302-22000-007-00D, Epidemiology and Management of Xylella fastidiosa (Xf)-caused Diseases and Xf Insect Vectors. Genetic diversity and population structures of PD Xf were analyzed by 30 SSR primers. Pierce disease-associated Xf population samples were collected from California representing four geographic populations of Napa, Sonoma and Kern and Riverside counties. Almond leaf scorch disease-associated Xf population samples were collected from orchard sites in Fresno and Kern counties. Haplotypes and allele frequencies from each population and subpopulations were recorded. Genetic distances for both host-associated Xf populations were estimated. These hierarchical analyses allow partitioning of the genetic differentiation among counties, within a county among sites, and within sites among individuals which characterize possible Xf population structures. Research continues building the allele frequency database using multilocus SSR markers. A state wide sampling effort has been performed for this purpose. This sampling strategy and genetic analyses are continuing to provide crucial information for understanding Xf population dynamics in temporal and spatial variations that will be useful for disease epidemiology and for developing an effective pest/disease management strategy.