In the present study, for investigating the molecular mechanism and related behavior in different handedness of mice, the most typical left and right handed mice were screened to extract the RNA from their motor cortex which used for microarray assay. By comparing the gene expression between left and right motor cortex from different handed mouse respectively, a series of candidate genes have been got. There are 15 in left-handed mouse and 106 in right-handed mice. We selected some ion channel receptor genes to verify and finally confirmed that GABA A-receptor mRNA in the right-handed mice is asymmetric expressed that the expression in the right cortex is higher than the expression in the left cortex. And its expression is not asymmetry in the left-handed mice. We further tested the mice on locomotor activity, depression and anxiety-like behavior, and found that right-handed mice in the elevated plus maze test spent significantly less time in exploring the open arm than left-handed mice. At the same time, we found that right-handed mouse has stronger neural plasticity, and is more sensitive for the long-term unilateral feeding training; and most of the left-handed mice are not impacted by the training. These results are reflected there have big differences between rights and left handed mice in the molecular and behavioral level. And it is not perceived as tradition that the left and right handed are mirroring. These data remind us that the handedness may not an outcome of the simply asymmetry of one structure or molecular in the brain.