An efficient and accurate general-purpose bisulfite sequence mapping program. BatMeth can be deployed for the analysis of genome-wide bisulfite sequencing using either base reads or color reads. It allows asymmetric bisulfite conversion to be detected by labeling the corresponding reference genome with the hit. It integrates novel mismatch counting, list filtering, mismatch stage filtering and fast mapping onto two indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools.