To investigate population structure and marker assisted breeding, fast isolation by AFLP of sequences containing repeats (FIASCO) and GenBank database mining were used to develop novel microsatellite markers for sea perch ( Lateolabrax japonicus
). Genomic DNA fragments containing SSR sequences were captured by hybridization to (GT)13 biotin-labeled probe and were ligated to PMD18-T vector. Among 150 randomly chosen clones from the SSR-enriched library, 66 sequences contained microsatellite motif over five repeats. In addition, 540 cDNA sequences and 132 ESTs of Lateolabrax japonicus were downloaded from GenBank and screened for di-, tri- and tetra-nucleotide repeats, while 22 sequences were found to contain microsatellites. As a result, 15 microsatellite loci were shown to be polymorphic in 30 Lateolabrax japonicus
individuals, with the alleles ranging from two to ten, the observed heterozygosities from 0.6000 − 1.0000, and the expected heterozygosities from 0.5079 − 0.8890. Four loci (SP17, SP52, SP94 and SP468) were deviated from HWE in the sampled population after Bonferroni’s correction, and no linkage disequilibrium was found among all loci (P<
0.003), whereas null alleles were detected at locus SP52 (P<
0.05). Among 15 polymorphic loci, the PIC values, which can be used for related population genetics analysis, were all above 0.5, with the exception of SP17 and SP468.