The function of genome methylation in invertebrates has only recently been characterized in-depth. In this study, we firstly investigated the associations of genome methylation level and growth traits inpearl oyster, Pinctada fucata (P. fucata). The incidence of type II locus (hemi-methylation locus) was significantly correlated with the shell height and the shell length, with Pearson correlation coefficients of 0.204 and 0.233, separately. The incidence of type IV locus (super methylated locus) on the other hand was significantly correlated with the shell length, with Pearson correlation coefficient of 0.217. The genome methylation levels were significantly positively correlated with shell height, shell length, shell width, total weight and shell weight (P<0.05). The incidence of type II locus (hemi-methylation locus) was also significantly positively associated with growth rates of the shell height and the shell length, and Pearson correlation coefficients were 0.268 and 0.298, respectively. The results indicated that genome methylation of P. fucata may play a pivotal role in the formation of growth trait, and could be considered for growth trait selection in breeding.