Mycosphaerella graminicola (anamorph: Zymoseptoria tritici, formerly Septoria tritici), the responsible for Septoria tritici blotch, is the most frequently occurring disease on wheat crops worldwide. The populations of this pathogen were previously characterized in several areas around the world, but not in Algeria so far. The present study aims thus at investigating the genetic diversity and population structure of M. graminicola in this country. One hundred and twenty monoconidial isolates of this fungus (60 from bread wheat and 60 from durum wheat) were collected during the 2012 growing season from five distinct geographical locations in Algeria. They were then fingerprinted using eight microsatellite markers. The number of alleles per locus ranged from 2 to 11, with an average of 6.25 alleles per locus. We found out a moderate gene diversity, a high genotype diversity (72% of unique haplotypes) and a low population differentiation within the population. Further analyses using both UPGMA and Bayesian clustering methods confirmed the lack of genetic structuration irrespective of geographical locations and host species. These findings are likely due to the frequent occurrence of sexual reproduction in the field, leading to genetic diversification and allele homogenization via wind born ascospores within the population.