Microwaves have emerged as a promising technology with wide range of applications across various fields, due to inconsistent results across various mutagenicity studies, the research intends to detect the impact of microwave radiation at 2450 MHZ on the morphological traits and molecular characteristics of Vicia faba L. seedlings exposed to different microwave exposure periods. Six treatments in three replicates were performed and the plant seeds were exposed to microwaves radiation at (0, 10, 20, 30, 40, 50 seconds) respectively, and then planted in the greenhouse and the morphological traits were recorded are (plant height, number of pods, number of seeds, weight of seeds, number of leaves and length and width of leaves). RAPD technique was used to evaluate the molecular variations among treatments. The results revealed the morphological traits (plant height, number of pods, leaf length and width) were positively affected and directly correlated with exposure time and were significantly increased compared with control sample while other traits (number of seeds, seeds weight and number of leaves) were negatively affected and inversely correlated with control where the measurements decreased with the increase of exposure time and were insignificant compared with the control sample except number of leaves which was significant. RAPD analysis revealed the occurrence of 67 unique and absent bands which reflected on growth performance. The study revealed the promising effect of microwaves on the vegetative traits at short term exposure, while long term exposure could inhibit the growth performance.