Laboratory studies were conducted to evaluate possible interactions of atrazine and glyphosate on soybeans at the molecular level. Because these compounds alter the extractable activities of nitrate reductase (NR)3 and phenylalanine ammonia-lyase (PAL), these enzymes were chosen as biochemical markers. Levels of anthocyanin, hydroxyphenolic compounds, and chlorophyll were also determined. Three-day-old dark-grown soybean seedlings, susceptible to both herbicides, were transferred to 2 mM CaSO4 or CaSO4 containing high-purity 10–4 M atrazine, 10–4M glyphosate, or a combination of both herbicides at 10–4 M each. Plants were placed in a growth chamber under continuous light (200 μE·m–2·s–1) at 25 C and harvested at 24-h intervals over a 96-h time course. Interactions of atrazine and glyphosate on hypocotyl elongation were detected after 96 h when the compounds were supplied simultaneously. Intermediate PAL levels were found in the atrazine + glyphosate treatment compared to the levels for each herbicide alone. At 96 h, anthocyanin content in hypocotyls in the atrazine + glyphosate treatment was twice that of the atrazine treatment, and hydroxyphenolic content was increased by 25% (per axis). Interactions of these herbicides were also apparent on NR activity; i.e., on a per organ basis the combination treatment resulted in levels 20% higher than glyphosate alone in roots and 16 times greater than glyphosate alone in leaves after 96 h. Total chlorophyll content in hypocotyls (μg/organ) was decreased by atrazine but not significantly by glyphosate after 96 h. Atrazine + glyphosate resulted in chlorophyll content equal to that of atrazine alone. Mathematical analyses showed that interactions on NR, PAL, anthocyanin levels, and hypocotyl elongation were antagonistic at 96 h. These data demonstrate interaction between atrazine and glyphosate in plant tissues that is related to some biochemical parameters associated with the secondary molecular mode of action of these herbicides.