This study carried out to examine the association between the haplotypes of mitochondrial control region (CR) and growth traits of two F1 progeny populations of the Red-spotted grouper. We found polymorphic patterns of the 133-bp repeat units in the CR. In the BBR01 population (70-days after hatching), a total of 1,091 F1 progeny were divided into three haplotypes (H01, H03 and H04). The significant differences were found in the levels of BL, BW and LWI (p<0.05). The F1 animals with the haplotype H01 had greater level of BL (50.815±4.586 mm) than those of H03 (47.270±6.486 mm) and H04 (47.179±6.278 mm). The H01 F1 fishes were heavier level of BW (2.270±0.559 g) than those of H03 (1.789±0.711 g) and H04 (1.797±0.706 g). In the BBR02 population (11-months after fertilization), three haplotypes H03, H04 and H05 were detected. The significant difference was found only in the BL values among three haplotypes (p<0.05). The F1 animals with the haplotype H03 had greater level of BL (19.22±2.000 cm) than those of H04 (18.64±1.964 cm) and H05 (18.86±1.512 cm). There were no significant differences in BW and LWI among haplotypes in the BBR02 population (p>0.05). These results suggested that the mitochondrial haplotypes may affect the growth traits during early developmental stage of the Red-spotted grouper. The marker-assisted selection system for broodstock animals may be helpful in improving performance traits for aquaculture of the Red-spotted grouper.