Large gene families and the frequent overlapping functions of homologous genes remain a major challenge for functional genetics in plants. In recent years, the development of homology-based gene silencing using computationally generated artificial microRNAs (amiRNAs) has been demonstrated to be a promising tool for functional genomics in plants. In this study, through a forward genetics screen, we isolated an abscisic acid-insensitive amiRNA line targeting five previously uncharacterized F-box Insensitive to ABA (FIA) genes. Notably, a triple mutant in the identified FIA genes FIA1, FIA3 and FIA4 (f1/f3/f4), that are expressed in germinating seeds, exhibited ABA insensitivity in the inhibition of seed germination. In contrast, this ABA insensitivity was not observed in a double mutant of two FIA genes FIA1 and FIA4 (f1/f4). Further investigation of the FIA1 interactome using F box decoy lines revealed the gibberellin (GA)-responsive GASA1 protein that has been reported to encode a small stress signaling peptide as an interacting partner. We found that abscisic acid promoted the ubiquitination of GASA1 in Arabidopsis, leading to its degradation via the 26S proteasome pathway. Together, our study reveals that abscisic acid represses seed germination through FIA proteins and regulates the FIA interactor, GA-responsive GASA1.