Such geochemical investigations of alkaline granites as both Wadi Sieh and Wadi Lethi, south Sinai, Egypt, indicate that they are A-type granites. They are similar in major and trace elements but differ in rare earth elements (REE). The alkaline granite of Wadi Sieh (AGS) is enriched in LREE whereas the alkaline granite of Wadi Lethi (AGL) is enriched by MREE and HREE. Zircon crystals on both AGS and AGL are studied using Scanning Electron Microscopy (SEM) and analyzed for major, trace and rare earth elements by electron microprobe in order to reveal the relation between whole-rock chemistry and zircon morphology and chemistry. The faces of zircons on both AGS and AGL are affected by alkaline magma during their crystallization period reflecting a development of {101} pyramidal faces. This study indicates that no relation is noticed between trace elements of zircon and whole-rock chemistry while, ΣREEs of zircon increases with increasing of phosphorus not with the ΣREE of whole-rock.