Didymella fabae is a highly destructive fungal pathogen of faba bean (Vicia faba) that represents a significant yield-limiting biotic constraint in all locations where the crop is grown. However, nothing is known about the population structure of this pathogen anywhere in the world. Population genetic analyses employing 18 sequence-tagged microsatellite (STMS) markers covering eight genetic linkage groups and a PCR-based mating type marker were used to elucidate the genetic structure and reproductive mode of the pathogen in three populations in Syria. High gene diversity within populations but low genetic differentiation among populations was observed and the entire collection of isolates was assigned to a single genetic population using a Bayesian clustering algorithm. Independent analyses were performed based on four unlinked sets of STMS markers to infer reproductive mode. A simulation approach was used to estimate which of the repeated multilocus genotypes were probably the result of asexual reproduction and should be clone-corrected. A 1:1 ratio of mating types could not be rejected in any clone-corrected population, probably due to small sample sizes. Likewise, frequency of clones and sample size, but not marker linkage, had strong effects on multilocus gametic disequilibrium. The null hypothesis of random mating was rejected in the majority of populations for both non-clone-corrected and clone-corrected samples and with four sets of unlinked markers indicating a predominance of asexual reproduction in these populations. This represents the first detailed screening of clonal and genetic composition of D. fabae populations in Syria.