Abstract DEHYDRATASE-ENOLASE-PHOSPHATASE−COMPLEX1 (DEP1), a trifunctional enzyme with dehydratase, enolase, and phosphatase activities, initially characterizes with its enzymatic function in the recycling of the ethylene precursor methionine (Met). Here, we identified an apple MdDEP1 gene, which encodes a protein highly homologous to Arabidopsis Yang’s cycle gene AtDEP1. GUS staining of 35S::pMdDEP1-GUS transgenic Arabidopsis showed that MdDEP1 is widely expressed in Arabidopsis tissues especially in vascular systems. Additionally, ectopic expression of MdDEP1 alters salt and drought tolerance, and triggers early flowering in Arabidopsis on the medium. The increase of salt tolerance in MdDEP1-expressing plants was realized through upregulation of the typical salt overly sensitive (SOS) pathway-related genes, including AtSOS1, AtSOS2, and AtSOS3; and that MdDEP1 controlled flowering time mainly by influencing the expression of flowering-associated genes. Collectively, these findings provide new functions of the DEP1 protein and its underlying mechanisms, in which MdDEP1 confers salt and drought-tolerance, and early flowering phenotypes.