Bismark is a flexible and efficient tool for analyzing Bisulfite-Seq (BS-Seq) data, combining read mapping and methylation calling in a single step. It distinguishes between cytosines in CpG, CHG, and CHH contexts, enabling researchers to quickly visualize and interpret methylation data after sequencing. Bismark is released under the GNU GPLv3+ license and is freely available online. It handles both directional and non-directional bisulfite libraries, accurately mapping reads and determining methylation states. The tool converts reads into C-to-T and G-to-A versions, aligning them to pre-converted reference genomes to determine strand origin. Bismark's output includes detailed information on mapping position, alignment strand, and methylation calls. It also provides a methylation extractor component for generating methylation data in various formats, including comprehensive or strand-specific outputs. The output can be visualized in genome browsers without requiring additional computational expertise. Bismark is user-friendly, highly flexible, and the first published BS-Seq aligner to handle both single- and paired-end mapping of directional and non-directional bisulfite libraries. It is designed for easy interpretation and direct analysis by researchers. Funding comes from the Biotechnology and Biological Sciences Research Council (BBSRC). No conflicts of interest are declared.Bismark is a flexible and efficient tool for analyzing Bisulfite-Seq (BS-Seq) data, combining read mapping and methylation calling in a single step. It distinguishes between cytosines in CpG, CHG, and CHH contexts, enabling researchers to quickly visualize and interpret methylation data after sequencing. Bismark is released under the GNU GPLv3+ license and is freely available online. It handles both directional and non-directional bisulfite libraries, accurately mapping reads and determining methylation states. The tool converts reads into C-to-T and G-to-A versions, aligning them to pre-converted reference genomes to determine strand origin. Bismark's output includes detailed information on mapping position, alignment strand, and methylation calls. It also provides a methylation extractor component for generating methylation data in various formats, including comprehensive or strand-specific outputs. The output can be visualized in genome browsers without requiring additional computational expertise. Bismark is user-friendly, highly flexible, and the first published BS-Seq aligner to handle both single- and paired-end mapping of directional and non-directional bisulfite libraries. It is designed for easy interpretation and direct analysis by researchers. Funding comes from the Biotechnology and Biological Sciences Research Council (BBSRC). No conflicts of interest are declared.