Many invasive weeds are known to create their deleterious effects on biological ecosystems and also rhizosphere soils. Weeds such as Cosmos and Xanthium have their existence near agricultural crops fields. Such weeds grow in abundance, releasing specific allelochemicals which have adverse effect on germination rate, physiological patterns and reproduction of crop plants. In present work, allelopathic effects of leaf leachates of Cosmos and Xanthium were observed on seed germination and seedling growth of Triticum aestivum, Vigna radiata and Trigonella foenum-graceum like crops. Seed germination was inhibited at higher concentration at 6% while lower concentrations showed stimulatory effect on Mungbean and Fenugreek from 1%-4% concentrations. But seed germination percentage of Vigna and Trigonella showed 70% and 60% growth in response to leaf leachates of Cosmos at 6% concentration. Triticum showed total inhibition of 40% to both leaf leachates. The qualitative phytochemical analyses showed presence of alkaloids, phytosterols, phenols, tannins and flavonoids. GCMS and IR studies revealed presence of major constituents such as esters, ethers, anhydride and polyalcohols. Cosmos and Xanthium showed the characteristic FTIR fingerprinting regions of various functional groups such as –OH, carbonyl, anhydride, ester and amides. The variations in phytochemicals of these invasive might be attributed to response of the plants to different environmental stresses.