Leaf rust caused by Puccinia triticina Eriks., is one of the most common diseases of wheat (Triticum aestivum L.)  in Egypt and worldwide. To investigate the population genetic structure of the causal pathogen, 468 single isolates were obtained from 193 samples collected from 12 Egyptian governorates and analyzed during 2016/17 and 2017/18 growing seasons. A total of 125 and 101 leaf rust pathotypes were designated during 2016/17 and 2017/18 growing seasons. The most frequent pathotype was STTTK (9.81% frequency), followed by race PTTNS (2.80% frequency) during 2016/17. While, pathotype PTTTT was occurred at a high frequency (12.16% frequency), followed by the four pathotypes; TTTBT, PTTGS, TTTTT and PTTCT (5.88, 5.10, 5.10 and 4.31%, respectively), during 2017/18. Pathotype STTTK is the most geographically distributed as it was detected in nine governorates in 2016/17, but in 2017/18, PTTTT is the most geographically distributed pathotype, where it was found in seven governorates. High similarity was found between leaf rust populations in the five locations, i.e. Domiatta, Sohag, Alexandria, Kafr El-Sheikh and Bani Sweif, during 2016/17 growing season. Also, high similarity was found between leaf rust pathogen populations of Kafr-Elsheikh, Sohag, Beheira, Dakahlia, Sharqiya, Domiatta, Gharbiya, Fayoum and Minufiy, during 2017/18 growing season. The phenotypic diversity within different populations under study was characterized using the three indexes; Shannon, Gleason and Simpson. Shannon index proved to be more suitable to accurately measure the phenotypic diversity between the tested populations of the causal pathogen, as it was sensitive to sample size, number of isolates, number of races and standard deviation of race frequency than the others.