Breeding is the basis for aquaculture, the seed selection and cultivation is an effective way to increase production. This study was conducted Gentian grouper Epinephelus lanceolatus breeding in traditional breeding and molecular markers to carry out. Application has been established SSR analysis gentian grouper. Test content growing trend analysis, MEF2D gene in the amount of scales performance, and microsatellites / SSRs applied gentian grouper. The results showed that Gentian grouper caudal scales higher amount of RNA. Different body size fish no significant difference in the amount of RNA. Microsatellites / SSRs application results showed four SSRs correlated with body weight.