Abstract:Black wheat had very important value in nutrition and wheat breeding,it was crossed by Chinese Spring and Elytrigia intemodium. In hybrid progeny, seed coat of the lines that we chose was stable black. The ten lines were 3-2, 3-3, 3-4, 3-11, 3-13, 3-33, 3-36, 3-37, 3-39 and 10-38. We conducted chromosome variation analysis and moleculor marker identification,the results showed that the diploid chromosome number of the most root-tip cells was 42, there were a few univalents and many bar bivalents in PMC metaphaseⅠ, a little lagging chromosonie, chromosome bridges and micronuleus were found in ana.Ⅰ, ana.Ⅱand tetraspore. Chromosomal abnormalities showed that the chromosome pairing was affected by the induction of E.intemodium chromosonie. Furthermore, we used RAPD and SCAR for identification, the results showed that the molecular marker OPF3 could amplify the specific molecularmarker of Eb genome of black wheat,3-2, 3-3 and 3-4, the molecular marker P3,P4 could amplify the specific molecularmarker of Ee genome of black wheat,3-11, 3-13, 3-33, 3-36, 3-39, 3-37 and 10-38. It can be deduced from the results that the 10 lines are translocation lines which have very important value in production and wheat breeding.