We propose a parallel algorithm that solves the best k-mismatches alignment problem against a genomic reference using the “one sequence/multiple processes” paradigm and distributed memory. Our proposal is designed to take advantage of a computing cluster using MPI (Message Passing Interface) for communication. Our solution distributes the reference among different nodes and each sequence is processed concurrently by different nodes. When a (putative) best solution is found, the successful process propagates the information to other nodes, reducing search space and saving computation time. The distributed algorithm was developed in C++ and optimized for the PLX and FERMI supercomputers, but it is compatible with every OpenMPI-based cluster. It was included in the ERNE (Extended Randomized Numerical alignEr) package, whose aim is to provide an all-inclusive set of tools for short reads alignment and cleaning. ERNE is free software, distributed under the Open Source License (GPL V3) and can be downloaded at: http://erne.sourceforge.net. The algorithm described in this work is implemented in the ERNE-PMAP and ERNE-PBS5 programs, the former designed to align DNA and RNA sequences, while the latter is optimized for bisulphite-treated sequences.