Gymnocypris przewalskii is the only kind of economic fishes distributed in Qinghai Lake located on the Qinghai Tibet plateau. Ribosomal protein S3a (RPS3a) is one kind of multifunctional protein known as a component of the 40s small ribosomal subunit. Research concerning molecular mechanism of Gymnocypris przewalskii  under salinity stress will contribute to discovering the basic pattern of vital activity and provide theories for conservation and artificial reproduction of this species. In this study, the cDNA sequences of RPS3a ［KC818610.1］ were obtained from the naked carp through reverse transcriptase polymerase chain reaction (RT-PCR) and 5′ and 3′ rapid amplification of cDNA ends (RACE-PCR). According to real time PCR analysis, the transcriptions of RPS3a increased in embryogenesis and under salinity stress, and it was demonstrated that RPS3a played an important role in embryogenesis and salinity adaptation.