The genetic diversity and population structure of Mycosphaerella pinodes (Dydimella pinodes) in Algeria were investigated by AFLP markers. A total of 75 isolates from different collection sites corresponding to four geographic regions were analyzed. Data from AFLP loci were used to estimate gene diversity, genetic distances, and to make indirect measures of gene flow between population groups. Extensive diversity was detected in the M. pinodes population regardless of the population group. The percentage of polymorphic loci varied from 41% in the semi-arid superior region to 50% in the sub-humid region. Nei’s gene diversity across loci was 0.471 and the Shannon’s index across loci was 0.663. A high level of differentiation (Gst = 0.308) and a low gene flow (Nm = 1.118) among population groups were found. Based on the analysis of molecular variance, 58% of the genetic variation of M. pinodes was within populations, 31% of the variation was between geographical regions and 11% among populations within a region. Cluster analyses using individual isolates failed to group them according to population. This is the first report on genetic diversity and population structure of M. pinodes on pea in Algeria.