Comprehensive knowledge of pathogen population structures is crucial to understand the epidemiology and history of infectious diseases, but such data is largely unavailable for plant pathogenic bacteria. This constitutes a challenge for genetically monomorphic bacteria. Xanthomonas citri pv. citri, which causes asiatic citrus canker, a major disease and potential threat of citrus worldwide, is listed as a quarantine organism in many countries. Analysis of the molecular epidemiology of this bacterium is hindered by a lack of molecular typing techniques suitable for surveillance and outbreak investigation. We report a comparative evaluation of two typing techniques, insertion sequence ligation-mediated PCR (IS-LM-PCR) typing and multilocus variable-number tandem-repeat analysis (MLVA), in terms of the information derived from the techniques and their effectiveness for analysis of genetic and population structure of 557 strains of X. citri pv. citri originating from Vietnam. The results were as follows: (1) a higher level of polymorphism was observed for MLVA as shown by the greater number of haplotypes and the higher value of Simpson's index of diversity for MLVA data; (2) Pairwise correlations between genetic distances among individual strains or pairwise population genetic differentiation were highly significant for two typing methods; (3) The two molecular markers yielded similar phylogenetic trees and population structure of X. citri pv. citri in Vietnam. These results provide guidance for the effective use of these molecular methods in the genetic analysis and epidemiology of Xanthomonas citri pv. citri at different temporal or spatial scales.