Sequence data from the article: A survey in natural olive resources exposed to high inoculum pressure indicates the presence of traits of resistance to Xylella fastidiosa in Leccino offspring.In this study, we described the transcriptome of three spontaneous olive genotypes, selected in the area of Apulia region heavily infected by Xylella fastidiosa subsp.pauca (Xf) for their limited symptoms, low bacterial populations, and very erratic distribution of twigs positive to Xf detection. Fifteen RNAseq libraries were constructed from five samples from each of the three olive plants and were analyzed to get insights on genes involved in plant defence response and resistance against Xf.