The use of forest tree species and weeds as green manure has exacerbated soil fertility issues, potentially due to the allelopathic chemicals present in these organic materials. Information available on their allelopathic potential on photosynthetic pigment, chlorophyll fluorescence and growth of soybean is not exhaustive. The objective was to determine the allelopathic effects of fresh leaf segments of L. camara and T. diversifolia on chlorophyll pigments and chlorophyll fluorescence of SB97 and SB19 soybean varieties. The experiment was carried out in the laboratory and greenhouse at Maseno University. In the lab, different concentrations of aqueous extracts, (25%, 50%, 75%, and 100%) and the control- tap water was used. Chlorophyll fluorescence and chlorophyll concentrations in plants were determined within a green house. Fresh leaf material of T. diversifolia and L. camara of 4g, 8g, 12g and 16g was added to soil in pots. The control only composed soil. This was replicated four times and laid out in Completely Randomized Design. Data on Chl a, a/b ratio, total chl, carotenoids, leaf maximum quantum yield and leaf effective quantum yield were recorded weekly. Data were subjected to analysis of variance using SAS 9.1 then treatment means were separated using LSD at P = 0.05. Chlorophyll fluorescence and chlorophyll concentration analyses revealed that both leaf biomass materials impacted negatively on photosynthetic activity of the soy bean varieties. Allelochemicals in the fresh leaf segments of these plants decreased maximum photochemical efficiency and quantum efficiency, potentially reducing photosynthetic activity. Farmers are therefore advised not to incorporate Lantana camara and Tithonia diversifolia leafy biomass in farms where soy bean varieties SB 19 and SB 97 are growing.