Chickpea is an important legume crop cultivated in many locations of Turkey and wild relatives of chickpea naturally grow in the Southeastern Anatolia Region of Turkey. Ascochyta blight caused by Didymella rabiei is one of the most important limiting factors for chickpea production. In this study, we aimed to investigate the genetic structures of D. rabiei samples from wild and domesticated chickpea hosts from different geographical regions. For this purpose, D. rabiei was collected from different geographic regions of Turkey between March and June in 2014 and 2015. Besides, some isolates were obtained from the wild chickpea species, C. pinnatifidum and C. reticulatum. Total, one hundred and two isolates of D. rabiei were genotyped using six sequence tagged microsatellite (STMS) markers. According to the results of molecular variance, the pathogen isolates from different geographic regions showed a significant genetic variation, but, most of which were confined within the populations. The total genetic diversity was estimated to be 0.612 for D. rabiei isolates from chickpea over the country. For the first time, D. rabiei from C. reticulatum, which is the wild ancestor of domesticated chickpea was found in the world and the isolates from C. reticulatum were represented with a single genotype. Isolates from C. pinnatifidum were genetically closer to the isolates from Southeastern Anatolia Region. All the isolates were grouped as one genetic population according to the Bayesian algorithm and presented a mixed distribution based on the principal coordinate analysis (PCoA) of genetic distances. All the results represented and updated the information about the genetic structure of D. rabiei populations across the country by announcing new information about the isolates from wild relatives. In addition, STMS markers were utilized to test whether allele sizes of microstallite loci change during asexual reproduction in infection period within the host. Thus, the changes in pathogen genotype was traced from seed to seedling. To do tracing, chickpea seeds were treated with two different D. rabiei isolates with known STMS multilocus genotypes. Then, pathogen re- isolations were performed from the plants grown from the infected seeds and these re-isolates were genotyped with the same STMS markers. Allele sizes of re-isolates were different from the parental ones for some of the loci which indicated that microsatellite alleles may have changed during multiple cycles of asexual reproduction through host infection.