Abstract: Epinephelus coioides is an important mariculture commercial fish in South China. In recent years, due to excessive fishing and rapid expansion of artificial breeding, the natural resources of E.coioides have declined and their genetic diversity has decreased. We applied random amplified polymorphic DNA (RAPD) and mitochondrial cytochrome b（Cyt b）gene sequences analyzing technique to three cultured stocks of E.coioides sampled from Huizhou, Shenzhen and Zhanjiang. The main results show that: 1）RAPD analysis might be more sensitive than mitochondrial Cyt b gene sequence to reveal genetic variations of E.coioides; 2）Compared with the other reported groupers, the genetic diversity of E.coioides might be affected by overfishing and aquaculture. The percentage of polymorphic loci was 40.57% according to RAPD analysis; 3）The genetic identity was 0.967 1~0.980 8 according to RAPD analysis and the nucleotide diversity of Cyt b was only 0.003 8. Small differentiation and similar genetic background were observed among E.coioides stocks. Furthermore, we explored the characteristics of mitochondrial Cyt b of E.coioides and put forward some suggestions and countermeasures for protecting genetic diversity of E.coioides.