The sequence-related amplified polymorphism (SRAP) molecular marker technique and BSA were used to Fenneropenaeus chinensis. The markers, which were based on differences between sensitive and tolerant samples, will be used to provide information and tools for the protection of the germplasm resource and for molecular marker-assisted breeding. We used 110 SRAP primers to screen for molecular markers. We selected 77 and 102 SRAP primers to screen ammonia nitrogen and pH-BSA gene pools, respectively. According to the frequency and pattern of bands in the samples, six markers associated with resistance to high ammonia nitrogen were selected; one from sensitive samples and five from tolerant samples. These markers ranged in length from 166 to 571 bp. Similarly, seven markers associated with resistance to high pH were selected; two from sensitive samples and five from tolerant samples. These 13 genetic markers were cloned into the pMD-18T vector, transformed into TOP10, and sequenced. The sequence data has been submitted to GenBank under the accession numbers GU570681–GU570693. Sequence and BLAST analyses showed that there was low similarity (<15%) between the markers and known functional genes, indicating that these markers are tightly linked to stress resistant traits but are not functional genes. Further research has been carried out to validate these results. These markers can be used to screen for stress resistance traits in