Cytosine DNA methylation is a stable epigenetic mark that plays a very important role in many biological processes, and is often responsible of phenotypic expressions. Bisulfite treatment of DNA is acknowledge as the gold standard technique to study methylation. Mapping bisulfite-treated reads to a reference genome represents a signiﬁcant computational challenge. GPU-BSM (standing for GPU-BiSulfite reads Mapping) is a GPU-based tool devised to map bisulfite-treated reads. It has been designed to support directional and non-directional libraries generated from both WGBS and RRBS. Basically, GPU-BSM adopts an unbiased strategy that reduces the complexity of involved sequences converting cytosines to thymines. Then, sequences represented with a simplified 3-letter nucleotide alphabet are aligned using the GPU-based SOAP3-dp short-read mapping tool.