Cyclic diguanylate monophosphate (c-di-GMP) is a second messenger that regulates multiple bacterial behaviors. It is synthesized by diguanylate cyclase (DGC) with the GGDEF domain, and degraded by phosphodiesterase (PDE) with the EAL or HD-GYP domain. The GepA (VP0117) protein in Vibrio parahaemolyticus contains both GGDEF and EAL domains, but its role remains unknown. This study found that deletion of the EAL domain or both the GGDEF and EAL domains in GepA increased intracellular c-di-GMP levels, enhanced biofilm formation, and inhibited polar flagellum-mediated swimming motility. Deletion of only the GGDEF domain had no such effects. Additionally, removing the EAL domain or both the GGDEF and EAL domains increased cpsA expression and decreased polar flagellar gene expression, while deleting the GGDEF domain alone had no impact on these genes. Overexpression of GepA or a GepA variant with a mutated GGDEF domain reduced biofilm formation but increased swimming motility. However, overexpression of GepA with a mutated EAL domain did not produce the expected phenotypic changes. In summary, GepA functions as a PDE to degrade c-di-GMP, thereby suppressing biofilm formation and enhancing swimming motility in V. parahaemolyticus.