Salinity is a major abiotic stress that often inhibits seed germination, growth, and development of crop plants. The salt-overly sensitive (SOS) regulatory pathway is a well-known mechanism that regulates ion homeostasis through the cooperative action of three critical components: SOS1 (Na+/H+-antiporter), SOS2 (Ser/Thr protein kinase), and SOS3 (Ca2+-binding protein). Although highly growth-defective sos mutant seedlings under salt-treated conditions were reported early, salt-dependent phenotypes for seed germination remain largely unknown. Here, we demonstrated that sos1, sos2, and sos3 mutants showed increased seed germination under saline conditions. Unlike in seedlings, SOS gene expression was not induced in seeds by salt treatment. The expression levels of ABA biosynthesis-related genes (NCED6 and NCED9) and ABA-signaling (ABI4 and ABI5) were impaired, and their salt inducibility was lower in the sos2 mutants than in the wild-type. Altogether, these results suggest that SOS proteins negatively regulate seed germination under saline conditions by disturbing ABA metabolism and signaling. Additionally, comparative transcriptome analysis of salt-treated seedlings and seeds revealed that although some of the stress-related genes were commonly regulated, different sets of genes are differentially altered in seeds and seedlings.