The spotted sea bass (Lateolabrax maculatus) is a valuable commercial mariculture fish in China and has huge potential for future genetic improvement. However, only limited number of SSR (simple sequence repeat) markers have been developed for L. maculatus. In this study, a total of 220,709 SSRs were identified from the L. maculatus genome. The total length, density and frequency of SSRs were 5,119,809 bp, 9898.28 bp/Mb and 425.06 loci/Mb, respectively. Dinucleotide repeats were predominant among SSRs (85.00 %) and AC was the most abundant SSR motifs. Both the number and length of SSRs in each chromosome were positively associated with the chromosome length. A total of 155,905 SSR markers were successfully designed (with an average of 6496 SSRs per chromosome). The frequency of SSR markers varied from 245.63 per Mb to 346.60 per Mb. 14 polymorphic SSR primers were used to evaluate the genetic diversity of L. maculatus wild population from Zhuhai. A total of 74 alleles were detected and most SSR markers showed high polymorphism information content (PIC). The cross-species transferability of 11 out of 67 tested loci were proven successful in largemouth bass Micropterus salmoides. The genome-wide SSRs and newly developed SSR markers made available in this study will facilitate future genetic breeding and genomic studies of spotted sea bass.