The mangroves, known as Earth's kidney, possess substantial ecological and commercial functions. Salinity stress is the most important abiotic stress restricting the growth and development of mangrove plants. Kandelia obovate, as the greatest latitudinally distributed true salt mangrove plant in China, was used for the studies of response to salt stress. Through different salt concentration stress treatment, a total of 7,591 salt stress-related genes were identified by RNA-seq. Combined with WGCNA analysis, 40 salt-related core genes were identified. This study provides a new idea for the molecular mechanism of salt stress.