As part of the California Regional PM2.5/PM10 Air Quality Study, annual average concentrations of PM2.5 associated organic compounds were measured using filter samples collected every sixth day for 24h for 1 year. During this time many central California sites had 24-h PM2.5 mass concentrations exceeding the National Ambient Air Quality Standard of 65μgm−3. The highest concentration of 175μgm−3 was recorded in Fresno on January 1, 2001. Organic speciation of 20 sites within and near the central California valley provides a measure of the spatial differences of emission sources through the use of organic molecular markers. Additionally, it provides an opportunity evaluate their utility at ambient concentrations to measure the influence of emission sources at rural and urban locations. The most abundant particulate phase organic compounds identified were polar organic compounds. Sugar anhydrates, molecular markers of wood combustion, constituted the largest weight fraction of total carbon, followed by alkanoic acids, and alkanedioic acids. Local emission sources such as residential wood combustion, gasoline and diesel vehicles were distinguished by unique molecular markers and found to vary among the annual average sites. The annual average concentrations of individual organic species within compound classes were observed to be highly correlated for many of the central California sites. The two Fresno sites were highly correlated to each other especially with respect to polycyclic aromatic hydrocarbons, but not well correlated to other sites.