Citrus canker, caused by pv. , is one of the most devastating bacterial diseases of citrus species. The global population of pv. includes three lineages designated as pathotypes A, A*, and A. Whereas pathotype A is the most prevalent lineage around the world, the citrus canker pathogen in Iran includes only pathotype A* strains. Previous work on the pv. strains collected before 2013 showed that two lineages of the pathogen were present in Iran (i.e., 4.1 and 4.4, with 4.4 not present anywhere else at that time). In this study, using a new set of strains collected in 2021 and 2022, we reassessed the population structure of the pathogen in Iran using a phylogeographic approach. All strains isolated in Iran still belonged to pathotype A*. Multilocus variable number tandem repeat analysis revealed that 62 Iranian strains collected between 1991 and 2022 were distributed among 22 haplotypes. Four new haplotypes were identified within the strains isolated in this study that have not previously been reported elsewhere in the world. Although all pre-2013 strains isolated in the Sistan-Baluchestan province of Iran were grouped in subcluster 4.4, and all post-2020 strains isolated in the same area were identified as members of subcluster 4.1. None of the post-2020 strains isolated in Iran belonged to subcluster 4.4, which suggests a shift in the population structure of the pathogen over the past two decades. Our data will pave the way for research on the population structure of the citrus canker pathogen in the area.