Technical Abstract: Green stem disorder of soybean [Glycine max (L.) Merr.] has increasingly become a nuisance for soybean producers. The disorder is distinguished from other manifestations of delayed plant maturity by the delayed senescence only of stems with normal pod ripening and seed maturation. The main objectives of this study were to compare the effects of fungicides with different chemistries and timing of fungicide application on incidence of green stem disorder using green stem disorder sensitive and insensitive soybean cultivars. Species of Diaporthe/Phomopsis and Macrophomina phaseolina were more frequent in stems without the disorder, whereas species of Colletotrichum were found mostly in stems with the disorder. Headline generally had a stronger effect than Domark in increasing incidence of the disorder, especially in green stem disorder sensitive cultivars, with over 50% incidence in many cases. Overall, the mid-season fungicide applications of Headline and a Domark-Headline mixture produced higher incidence of green stem disorder than early or late-season applications. Significant (P < 0.01) location x cultivar interaction occurred in all field experiments. Higher percent green stem disorder and higher yields were significant (P < 0.05), had positive regression slopes in 11 of the 28 trials, and was depended on soybean cultivar and location. From the results of this study, soybean producers should be aware of the possible risk that fungicide application may have in increasing incidence of green stem disorder. In addition, producers can help manage green stem disorder by selecting soybean cultivars reported to be consistently insensitive to the disorder.