In order to investigate the allelophatic effects of shoot and root aqueous extract of Johnson grass (Sorghum halepense L.) and pigweed (Amaranthus retroflexus L.) on seed germination and seedling characteristic of Sorghum and Wheat, a research was conducted based on completely randomized design with four replications. Treatments were four levels (25, 50, 75 and 100%) of leaf, stem, flower and root water extracts weeds (S halepense L.) and (A retroflexus L.) with distilled water as control. Results showed that there were allelopathic effects in Velvet flower and Johnson grass, effect of aqueous extract of different plant parts on germination traits of Sorghum and Wheat was not similar. Increasing the aqueous extract concentrations of separated Velvet flower and Johnson grass plant parts significantly inhibited Sorghum and Wheat percentage and rate of germination, length of radical and hypocotyls and increased time to 10 and 90% of germination. The degree of allelopathic effects of different Velvet flower and Johnson grass plant parts can be classified in order of decreasing inhibition as follows: stem, leaf, flower and root, and between two medicinal plants, Johnson grass indicated more allelopathic effects on germination traits.