Citrus bacterial canker (CBC) has become one of the most important diseases in many citrus cultivation areas, including Saudi Arabia (SA). This work aimed to characterize the genetic diversity of Xanthomonas citri pv. citri (Xcc) in SA by microsatellite and minisatellite analysis based on CRISPR typing. Our data revealed a high genetic infra-pathovar diversity of Xcc in SA, consistent with a recent analysis targeting tandem repeats (MLVA). Our finding showed that SA hosted 15 spoligotypes out of 63 spoligotypes recorded worldwide. Interestingly, we noted 10 new spoligotypes, two detected in the western region and eight in the south-western region. Two new spoligotypes were detected in Yemen. This finding suggests that the south-western region of SA was probably the source of Xcc variations in SA. Sequencing of the CRISPR regions confirmed the presence of Xcc Pathotype A recently identified in SA based on tandem repeat genotyping. Globally, our study supported the application of CRISPR-based sequence analysis for molecular epidemiology studies of Xcc and the usefulness of CRISPR typing to complement other typing tools, such as minisatellite typing.