Highly laborious plating of cultures onto solid media is inevitable in conventional yeast two-hybrid systems. We have successfully developed Liquid Y2H-Seq, a method which replaces solid media with liquid media for culturing and that displaces visual inspection of colonies with sequencing. Soybean (Glycine max) is a typical photoperiod-sensitive crop, meaning that specific duration light regime has a huge impact on soybean flowering and production. We obtained a lot of putatively interactions for soybean flowering genes. Finally, these reports introduce a labor-reducing and time-saving method for identifying protein-protein interactions, based on simple modifications to a ubiquitous protocol in life science research.