Abstract The aim of this study was to compare haploid and diploid embryo structure derived from two different wheat varieties, Triticum aestivum L. (Gün 91) and Triticum durum Desf. (Mirzabey). For diploid embryos, plants were grown until earing time, dicamba and 2,4-D were also applied to spikes in flowering period and embryos were collected after 18th-21st days of following pollination. For haploid plants, embryo rescue technique was used to derive haploid embryos by using intergenic crosses between both wheat varieties and corn (Zea mays L.). Synthetic auxins were also used to support of haploid embryo production. Two different microscopic measurement, width and length, were taken in each of embryo obtained. The decreasing in width of embryo in dicamba treatment group and also in length of embryo in 2,4-D treatment group were found to be different significantly (p<0.05 and p<0.01) in Gün 91 wheat variety. On the other hand, in Mirzabey, the decreasing of embryo length was also found to be shorter significantly (p<0.05) in 2,4-D treatment group than that of other groups studied. A total of 576 florets were crossed with maize and 0.52% of the florets produced haploid embryos across the two varieties. It was found that the measured sizes of diploid embryos were bigger than that of the haploid embryos as follows: width (60.68%) and length (47.52%) .There was no study about the structure of haploid embryo anatomically.