Open AccessThe occurrence of boron toxicity becomes a major constraint in cereal production in the world, thus cause significant yield loss particularly in wheat, one of the most susceptible crops to boron toxicity. Development of tolerant variety is now of utmost importance since agronomic management of soil boron is becoming ineffective to mitigate the toxicity. Due to narrow genetic base of the existing wheat cultivars, genetic variation for this character was poorly reported. The present study was devoted to identify such variation by using two different genetic background of wheat including Aegilops and Triticum, which could be readily used in wheat breeding program. Morphological and genetic screening revealed that two species Ae. longissima and Ae. sharonensis expressed tolerance against boron toxicity. The molecular marker analysis such as unweighted pair group method and principal coordinate analysis confirmed these two species to be more tolerant to excessive boron with higher root length. Their derivatives genotypes TL-09 and TL-17 were found to explained considerable tolerance to boron. On other hand, among the SSR markers used, Xgwm192 was the most robust in identifying boron tolerance polymorphism. The diversity and variability observed in this work could open new avenue in developing B toxicity tolerant wheat variety.