Thirty isolates of Xanthomonas oryzae pv. oryzae were collected from different rice-producing area in northern Thailand. For the assessment of genetic variation of bacterial blight pathogen, 19 primer combinations of amplified fragment length polymorphism primer system were screened to evaluate the genetic diversity and five combinations were selected according to their producibility, number of scorable bands and differences detected among representative isolates. Six lineages of X. oryzae pv. oryzae were identified in northern Thailand base on location. Lineage A composed of members from two provinces, Phitsanulok and Chainat. Lineage B was from various provinces as Sukhothai, Phetchaboon, Phicit, Phayao and Phrae. Lineage C was from Phitsanulok and Phrae. Lineage D comprised of members from Phrae, Chiangmai and Chiangrai while the lineage E composed of isolates from Sukhothai and Phitsanulok. The final lineage, lineage F, was from Lampang. Lineages B and D were the most widely distributed while lineage E seemed to be restricted to specific planting area. Wide distribution of the pathogen might be due to seed allocation and germplasm exchanged. Analysis showed that diversity of pathogen is due to single field and cultivars-specific effects. The results of this study will facilitate the use of effective bacterial blight resistance gene in northern Thailand.