Xylella fastidiosa is the causal agent of almond leaf scorch disease (ALSD), which is currently reemerging in California as a potential threat to almond (Prunus dulcis) production. We previously reported the presence of different colony morphotypes of X. fastidiosa ALSD strains on periwinkle wilt medium solidified with Gelrite and their association with genotypes or pathotypes after a low number of serial transfers. The morphotypes could be differentiated by single nucleotide polymorphisms and were classified as A- and G-genotypes. The stability of colony morphology was not studied. Yet, it is an important issue in the bacterial characterization. In this project, we evaluated the variations of colony morphology through 14 subculture passages. The G-genotype strains were consistently (>99%) associated with smooth colony morphotypes. Similarly, A-genotype strains were consistently associated with rough colony morphotypes. Rough A-genotype strains reversed to smooth colony variants at a low frequency suggesting phase variation in X. fastidiosa. In an ALSD survey, we successfully used colony morphology to discern X. fastidiosa genotypes with >95% accuracy. The phenotypic traits described in this study are of value for further biological and genetic studies of X. fastidiosa.