Abstract: This experiment was conducted to analyze the extent and pattern of cytosine methylation in porcine genome and the difference of methylation between the parents and their F1 hybrids. The extent and pattern of cytosine methylation was assessed in genomes from 6 Landrace boars, 50 Guangdong Lantang sows and 51 their F1 hybrids by using the technique of methylationsensitive amplified polymorphism(MSAP). A total of 1 074 DNA fragments including CCGG sites were amplified using 20 pairs of selective primers, in total, 415 methylated bands (sites) including 79 polymorphic bands were obtained, and the average proportion of methylation polymorphism（p） was 7.4%. The results demonstrated that DNA methylation extents were high and methylation level varied among the three populations, genomic DNA methylation level of male parents, female parents and their F1 hybrids were 27.7%, 27.8% and 25.1%, respectively; and the external cytosine methylation frequecy of the CCGG sequence in single strand DNA（208%） was higher than that in single or double strand DNA (17.9%). The results indicate MSAP technique is efficient for detecting cytosine methylation in porcine genomes, and the methylation polymorphism in pigs is high, and the genome methylation level of F1 hybrids was different from their parents.