DNA methylation difference of eleven tissues of Oreochromis mossambicus, Oreochromis hornorum and “ Mohe” hybrid tilapia (O. mossambicus♀×O. hornorum♂), such as skin, muscle and gill etc. was analyzed to explore the change of methylation pattern during the interspecific hybridization using methylation sensitive amplified polymorphism (MSAP). 16 pairs of primers were used to amplify selectively. The results of electrophoretic banding analysis showed that there were differences in the methylation levels among these different tissues of the same species and between the same tissues among “ Mohe” hybrid tilapia and its parents; the average methylation level of these tissues from O. mossambicus, O. hornorum and “ Mohe” hybrid progenies was 32.21%, 38.03% and 29.77%, respectively. The methylation level of hybrid progenies was lower than those of the parental progenies. Most of the methylation patterns of the hybrid progenies were similar to the parental progenies (A, B and C types, 19.67%, 29.99% and 25.42%), while 24.92% cytosine demethylation and hypermethylation were found in the genome of hybrid progenies and the number of demethylation sites (E type, 15.73%) was greater than that of hypermethylation sites (D type, 9.19%). These results suggested that the genomic DNA hypomethylation and the reshuffling of the DNA methylation pattern in the hybrid progenies might be associated with the heterosis. The present findings established epigenetic foundation to further reveal the heterosis mechanism of tilapia.