The present study aimed to evaluate the effects of Cd and Cr as separate and in combinations in hydroponically grown seedlings of FA‐08 and SH‐13 cultivars of wheat (Triticum aestivum L.). The concentrations of heavy metals were higher in the root as compared to shoot and were more pronounced in SH‐13 than FA‐08 cultivar. The decrease in the seedling length and biomass was observed when the metals were applied in combined form (Cd–Cr 80–120, Cd–Cr 100–120, Cr–Cd 140–80, and Cr–Cd 140–100). There were more declines in root length in the cultivar SH‐13 as compared to the shoot length, as the concentration of HMs increased. The root at level Cr‐140 and shoot at level Cd‐100 showed more reduction in SH‐13 than FA‐08. The high concentration of Cd and Cr affected the root epidermis, the cortical cells, and the xylem vessel. The size and number of stomata, length of long cells and short cells, and trichome were reduced at the concentration Cd‐100 and Cr‐140. The present study showed that the higher concentration of Cd and Cr affects the morpho‐anatomical features of both selected wheat cultivar moderately.