Wheat leaf rust caused by Puccinia triticina, is the most common and widely distributed wheat rust in the world. In order to study the genetic structure of leaf rust population 14 pairs of AFLP and 6 pairs of FAFLP primers evaluated on 86 isolates samples collected in Iran during spring of 2009. Results showed that almost all investigated isolates were genetically different and special pattern of AFLP allele's that confirm high genetic diversity within leaf rust population was observed. Analyses showed, all provinces were classified into three major groups particularly similar clusters were found between then neighboring provinces. Rust spore can follow the migration pattern in short and long distances to neighbor in provinces. Results indicated that the greatest variability was revealed by 97% of genetic differentiation within leaf rust populations and the lesser variation of 3% was observed between the rust populations. These results suggested that each population was not completely identical and high gene flow has occurred among the leaf rust population of different provinces. The highest differentiation and genetic distance among the Iranian leaf rust populations was detected between leaf rust population in Sistan and Baluchistan and highest similarity was observed between in Ardabil provinces. The high pathogenic variability of leaf rust races in Ardabil and Northern Khorasan may be an indication that these two regions are the center of origin of pathogenic arability. Present study shows that leaf rust population in Iran is highly dynamic and variable.