The Fertile Crescent is the centre of domestication of chickpea (Cicer arietinum) and also the place of origin of its pathogens. Agrosystems provide different environments to natural eco-systems, thus imposing different types of selection on pathogens. Here, the genetic structure and in vitro temperature growth response of the chickpea pathogen Didymella rabiei from domesticated chickpea (59 isolates from Turkey and 31 from Israel) and wild Cicer spp. (three isolates from Turkish C. pinnatifidum and 35 from Israeli C. judaicum) were studied. Six sequence-tagged microsatellite site (STMS) primer pairs were used to determine the genetic structure of the 128 D. rabiei isolates. Turkish isolates exhibited the highest genetic diversity (H = 0.69). Turkish and Israeli D. rabiei from domesticated chickpea were genetically closer to each other than isolates from the wild Cicer spp. Analysis of molecular variance showed that 54% of the genetic variation resided between isolates from wild and domesticated origins. EF1-alpha sequences distinguished between D. rabiei isolates from domesticated and wild Cicer spp. by four polymorphic sites. Nevertheless, a certain degree of mixing between isolates from wild and domesticated origin was demonstrated using the Bayesian algorithm as well as with principal coordinates analysis. Isolates sampled from domesticated chickpea from both countries were better adapted to temperatures typical of Levantine spring and had a significantly larger colony area at 25 degrees C than at 15 degrees C (typical Levantine winter temperature). These observations were in accordance to the heritability values of the temperature growth response.