Almond leaf scorch disease (ALSD) caused by Xylella fastidiosa is potentially a serious threat to the almond industry in San Joaquin Valley of California. Knowledge of X. fastidiosa behaviour in the plant host under field conditions is important for disease control and this issue is being addressed in this project. Occurrence of ALSD is strongly influenced by environmental factors. In 2006, the earliest leaf scorching symptoms were observed in June, whereas in 2007, the earliest occurrence of leaf scorching symptoms was in July, a delay of 1 month. In both years, PCR detected X. fastidiosa 1 month before of symptom expression. PCR was slightly more sensitive than cultivation method for early bacterial detection. However, uneven bacterial distribution and random sampling errors may have contributed to the differences among the assays. Correlation between cultivation and PCR detection was greater than 90%. During the processing of a large number of samples, we noticed occasional failures in PCR amplifications of some samples, interfering result interpretation. We developed an array-PCR protocol using primers from seven housekeeping genes to correct the deficiency.