Abalones are edible shellfish and a valuable food source in Asian countries. Although substances from abalone have bioactivities, such as anti-oxidation and anti-inflammation, anti-metastatic effects of abalone have not been fully revealed. Gastric cancer is a common malignant cancer, but prognosis is poor because of its high metastatic characteristics. In this study, a novel peptide (A2) from abalone (Haliotis discus hannai) was applied to investigate its antimetastatic effects in MKN-28 gastric cancer cells. Enhanced activities of glycogen-synthase kinase 3β(GSK-3β) by A2 treatment contributed to modulation of β-catenin; hence, β-catenin signaling was downregulated, and translocation of β-catenin to the nucleus was repressed. Moreover, cellular protrusions including lamellipodia and filopodia were disrupted through downregulation of Rac1 and Cdc42 in response to A2 in MKN-28 cells. It is suggested that A2 inhibits cell migration through controlling levels of β-catenin, GSK-3β, and also induced disorganization of lamellipodia and filopodia. Therefore, A2 possesses therapeutic properties to treat gastric cancer.