The Pacific oyster () inhabits the intertidal zone and shows tolerance to air exposure conditions. Most marine invertebrates have been demonstrated to suffer large-scale mortality following sudden changes in osmolality, causing huge economic losses to commercial aquaculture. To explore the effect of air exposure on the genomic DNA methylation of marine shellfish, methylation polymorphisms in genomic DNA in the Pacific oyster were analyzed using the fluorescence-labeled methylation sensitive amplified polymorphism (F-MSAP) technique. The oysters were exposed to air individually for 0 d, 0.5 d, 1 d, 3 d, 5 d, 7 d, 9 d, and 11 d. The incidence of DNA methylation in adductor and gill tissue was 29.76% and 29.82%, respectively, in the control group (day 0). Compared with the control group, the level of total methylation in various groups under air exposure increased initially, after which it decreased. The total level of methylation on days 0.5, 1, 3, 5, 7, 9, and 11 was 36.59%, 38.86%, 43.02%, 39.30%, 51.13%, 46.79%, and 35.06%, respectively, in adductor tissues and 39.3%, 42.13%, 39.36%, 43.54%, 56.19%, 38.57%, and 28.99%, respectively, in gill tissues. The methylation level on day 7 was higher than that following other air exposure durations (<0.05); at the end of the experiment (11 d), the methylation level nearly returned to that of the control. Moreover, data regarding genomic DNA methylation mutation patterns at CCGG sites were not consistent with cytosine methylation patterns and patterns of variation between adductor and gill tissue; hypermethylation sites were more numerous than demethylation sites (<0.05), indicating that remarkable changes occurred in the hypermethylation sites of the Pacific oyster. The results of the present study implied that the alteration of methylation patterns in in response to air exposure might be strongly linked to stress resistance. These studies are fundamental to direct further research regarding DNA methylation in the aquatic shellfish epigenome, specific gene expression, and stress tolerance.