The DNA methylated states in muscle tissues from Beijing You chicken were analyzed using methylation sensitive amplified polymorphism (MSAP) combined with fluorescence labeling and capillary electrophoresis technology. We optimized the MSAP experimental condition including the genomic DNA concentration, dilution of pre-amplification prod-uct, the internal standard content and the concentrations of selective primers, Mg2+ and dNTPs. Repeated experiments showed that this method can automatically detect the global DNA methylation states in Beijing You chicken, and can be extended to other animals or plants with complex genomes and rich methylation polymorphism.