Bell pepper (Capsicum annuum L.) is an important vegetable crop. But it is infected by various diseases caused by viruses, bacteria, fungi and pseudofungi, in particular the oomycete Phytophthora capsici Leonian. We studied, in-vitro antifungal properties of Ageratum conyzoides L. and Parthenium hysterophorus L. leaf extracts in different solvents (ethanolic, methanolic, acetonic and chloroform) against P. capsici causal agent of blight disease in Capsicum annuum. Acetone and chloroform extracts were very inhibitory. These extracts from Parthenium and Ageratum at 10 % most effectively inhibited the P. capsici when used as biofungicide. The low standard deviations in acetone and chloroform solvents, indicated results reliability and consistency and supported the Permanova analysis and associated p-values. The detection of biomolecule composition using FTIR spectroscopy was accurate and sensitive.